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Kim B, Piao R, Lee G, Koh E, Lee Y, Woo S, Jiang W, Septiningsih EM, Thomson MJ, Koh HJ. OsCOP1 regulates embryo development and flavonoid biosynthesis in rice (Oryza sativa L.). Theor Appl Genet 2021; 134:2587-2601. [PMID: 33950284 PMCID: PMC8277627 DOI: 10.1007/s00122-021-03844-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/22/2021] [Indexed: 06/07/2023]
Abstract
Novel mutations of OsCOP1 were identified to be responsible for yellowish pericarp and embryo lethal phenotype, which revealed that OsCOP1 plays a crucial role in flavonoid biosynthesis and embryogenesis in rice seed. Successful production of viable seeds is a major component of plant life cycles, and seed development is a complex, highly regulated process that affects characteristics such as seed viability and color. In this study, three yellowish-pericarp embryo lethal (yel) mutants, yel-hc, yel-sk, and yel-cc, were produced from three different japonica cultivars of rice (Oryza sativa L). Mutant seeds had yellowish pericarps and exhibited embryonic lethality, with significantly reduced grain size and weight. Morphological aberrations were apparent by 5 days after pollination, with abnormal embryo development and increased flavonoid accumulation observed in the yel mutants. Genetic analysis and mapping revealed that the phenotype of the three yel mutants was controlled by a single recessive gene, LOC_Os02g53140, an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). The yel-hc, yel-sk, and yel-cc mutants carried mutations in the RING finger, coiled-coil, and WD40 repeat domains, respectively, of OsCOP1. CRISPR/Cas9-targeted mutagenesis was used to knock out OsCOP1 by targeting its functional domains, and transgenic seed displayed the yel mutant phenotype. Overexpression of OsCOP1 in a homozygous yel-hc mutant background restored pericarp color, and the aberrant flavonoid accumulation observed in yel-hc mutant was significantly reduced in the embryo and endosperm. These results demonstrate that OsCOP1 is associated with embryo development and flavonoid biosynthesis in rice grains. This study will facilitate a better understanding of the functional roles of OsCOP1 involved in early embryogenesis and flavonoid biosynthesis in rice seeds.
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Affiliation(s)
- Backki Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Rihua Piao
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, 136100 China
| | - Gileung Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Eunbyeol Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Yunjoo Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Sunmin Woo
- College of Pharmacy and Research Institute of Pharmaceutical Science, Seoul National University, Seoul, 08826 Republic of Korea
| | - Wenzhu Jiang
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062 China
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
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Lee G, Piao R, Lee Y, Kim B, Seo J, Lee D, Jang S, Jin Z, Lee C, Chin JH, Koh HJ. Identification and Characterization of LARGE EMBRYO, a New Gene Controlling Embryo Size in Rice (Oryza sativa L.). Rice (N Y) 2019; 12:22. [PMID: 30972509 PMCID: PMC6458227 DOI: 10.1186/s12284-019-0277-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/11/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Although embryo accounts for only 2-3% of the total weight of a rice grain, it is a good source of various nutrients for human health. Because enlarged embryo size causes increase of the amount of nutrients and bioactive compounds stored within rice grain, giant embryo mutants of rice (Oryza sativa L.) are excellent genetic resources for improving the nutritional value of rice grains. RESULTS Three giant embryo mutants, including large embryo (le), giant embryo (ge) and super-giant embryo (ges), with variable embryo size were used in this study. We investigated whether genes controlling embryo size in these mutants (le, ge and ges) were allelic to each other. Although ge and ges was allelic to GIANT EMBRY (GE), le was not allelic to ge and ges in allelism test. The GE gene carried a unique nucleotide substitution in each of the two mutants (ge and ges), resulting in non-synonymous mutations in exon 2 of GE in both mutants. However, the GE gene of the le mutant did not carry any mutation, suggesting that the enlarged embryo phenotype of le was governed by another gene. Using map-based cloning, we mapped the LE gene to the short arm of chromosome 3. The le mutant showed mild enlargement in embryo size, which resulted from an increase in the size of scutellar parenchyma cells. The LE encodes a C3HC4-type RING finger protein and was expressed to relatively high levels in seeds at a late developmental stage. Knockdown of LE expression using RNA interference increased the embryo size of rice grains, confirming the role of LE in determining the embryo size. CONCLUSION Overall, we identified a new gene controlling embryo size in rice. Phenotypic and molecular characterization results suggest that the le mutant will serve as a valuable resource for developing new rice cultivars with large embryos and nutrient-dense grains.
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Affiliation(s)
- Gileung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Rihua Piao
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100 Jilin China
| | - Yunjoo Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Backki Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Jeonghwan Seo
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Dongryung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Su Jang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Zhuo Jin
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Choonseok Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Joong Hyoun Chin
- Graduate School of Integrated Bioindustry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006 South Korea
| | - Hee-Jong Koh
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
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Lee Y, Choi MS, Lee G, Jang S, Yoon MR, Kim B, Piao R, Woo MO, Chin JH, Koh HJ. Sugary Endosperm is Modulated by Starch Branching Enzyme IIa in Rice (Oryza sativa L.). Rice (N Y) 2017; 10:33. [PMID: 28730411 PMCID: PMC5519516 DOI: 10.1186/s12284-017-0172-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/10/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Starch biosynthesis is one of the most important pathways that determine both grain quality and yield in rice (Oryza sativa L.). Sugary endosperm, sugary-1 (sug-1), is a mutant trait for starch biosynthesis. Rice plants carrying sug-1 produce grains that accumulate water-soluble carbohydrates instead of starch, even after maturity. Although this trait enhances the diversity of grain quality, sugary endosperm rice has hardly been commercialized due to the severely wrinkled grains and subsequent problems in milling. This study was conducted to identify the genes responsible for the sug-h phenotype through a map-based cloning technology. RESULTS We induced a mild sugary mutant, sugary-h (sug-h) through the chemical mutagenesis on the Korean japonica cultivar Hwacheong. Grains of the sug-h mutant were translucent and amber-colored, and the endosperm appeared less wrinkled than sug-1, whereas the soluble sugar content was fairly high. These characteristics confer greater marketability to the sug-h mutant. Genetic analyses indicated that the sug-h mutant phenotype was controlled by a complementary interaction of two recessive genes, Isoamylase1 (OsISA1), which was reported previously, and Starch branching enzyme IIa (OsBEIIa), which was newly identified in this study. Complementation tests indicated that OsBEIIa regulated the properties of sugary endosperm. CONCLUSIONS Complementary interactions between the starch biosynthesis genes OsISA1 and OsBEIIa determine the mild sugary endosperm mutant, sugary-h, in rice. Our finding may facilitate the breeding of sugaryendosperm rice for commercial benefit.
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Affiliation(s)
- Yunjoo Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Min-Seon Choi
- Vegetable Crop Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Muan, 534-833 South Korea
| | - Gileung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Su Jang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Mi-Ra Yoon
- Department of Central Area Crop Science, National Institute of Crop Science (NICS), RDA, Suwon, 16429 South Korea
| | - Backki Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Rihua Piao
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin 136100 China
| | - Mi-Ok Woo
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Joong Hyoun Chin
- Graduate School of Integrated Bioindustry, Sejong University, 209, Neungdong-ro Gwangjin-gu, Seoul, South Korea
| | - Hee-Jong Koh
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
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Piao R, Iguchi S, Hamada M, Matsumoto S, Suematsu H, Saito AT, Li J, Nakagome H, Takao T, Takahashi M, Maeda H, Yanagisawa Y. High resolution NMR measurements using a 400MHz NMR with an (RE)Ba2Cu3O7-x high-temperature superconducting inner coil: Towards a compact super-high-field NMR. J Magn Reson 2016; 263:164-171. [PMID: 26778351 DOI: 10.1016/j.jmr.2015.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 06/05/2023]
Abstract
Use of high-temperature superconducting (HTS) inner coils in combination with conventional low-temperature superconducting (LTS) outer coils for an NMR magnet, i.e. a LTS/HTS NMR magnet, is a suitable option to realize a high-resolution NMR spectrometer with operating frequency >1GHz. From the standpoint of creating a compact magnet, (RE: Rare earth) Ba2Cu3O7-x (REBCO) HTS inner coils which can tolerate a strong hoop stress caused by a Lorentz force are preferred. However, in our previous work on a first-generation 400MHz LTS/REBCO NMR magnet, the NMR resolution and sensitivity were about ten times worse than that of a conventional LTS NMR magnet. The result was caused by a large field inhomogeneity in the REBCO coil itself and the shielding effect of a screening current induced in that coil. In the present paper, we describe the operation of a modified 400MHz LTS/REBCO NMR magnet with an advanced field compensation technology using a combination of novel ferromagnetic shimming and an appropriate procedure for NMR spectrum line shape optimization. We succeeded in obtaining a good NMR line shape and 2D NOESY spectrum for a lysozyme aqueous sample. We believe that this technology is indispensable for the realization of a compact super-high-field high-resolution NMR.
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Affiliation(s)
- R Piao
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan; Graduate School of Engineering, Chiba University, Chiba 236-8522, Japan
| | - S Iguchi
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan; Faculty of Science and Technology, Sophia University, Yotsuya 102-8554, Japan
| | - M Hamada
- Japan Superconductor Technology, Inc., Kobe, Hyogo 651-2271, Japan
| | - S Matsumoto
- Superconducting Wire Unit, National Institute for Materials Science, Tsukuba 305-0003, Japan
| | - H Suematsu
- JEOL RESONANCE Inc., Akishima, Tokyo 196-8558, Japan
| | - A T Saito
- Graduate School of Engineering, Chiba University, Chiba 236-8522, Japan
| | - J Li
- Graduate School of Engineering, Chiba University, Chiba 236-8522, Japan
| | - H Nakagome
- Graduate School of Engineering, Chiba University, Chiba 236-8522, Japan
| | - T Takao
- Faculty of Science and Technology, Sophia University, Yotsuya 102-8554, Japan
| | - M Takahashi
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan
| | - H Maeda
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan
| | - Y Yanagisawa
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan; Graduate School of Engineering, Chiba University, Chiba 236-8522, Japan.
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Yanagisawa Y, Piao R, Iguchi S, Nakagome H, Takao T, Kominato K, Hamada M, Matsumoto S, Suematsu H, Jin X, Takahashi M, Yamazaki T, Maeda H. Operation of a 400MHz NMR magnet using a (RE:Rare Earth)Ba 2Cu 3O 7-x high-temperature superconducting coil: Towards an ultra-compact super-high field NMR spectrometer operated beyond 1GHz. J Magn Reson 2014; 249:38-48. [PMID: 25462945 DOI: 10.1016/j.jmr.2014.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 10/01/2014] [Accepted: 10/05/2014] [Indexed: 06/04/2023]
Abstract
High-temperature superconductors (HTS) are the key technology to achieve super-high magnetic field nuclear magnetic resonance (NMR) spectrometers with an operating frequency far beyond 1GHz (23.5T). (RE)Ba2Cu3O7-x (REBCO, RE: rare earth) conductors have an advantage over Bi2Sr2Ca2Cu3O10-x (Bi-2223) and Bi2Sr2CaCu2O8-x (Bi-2212) conductors in that they have very high tensile strengths and tolerate strong electromagnetic hoop stress, thereby having the potential to act as an ultra-compact super-high field NMR magnet. As a first step, we developed the world's first NMR magnet comprising an inner REBCO coil and outer low-temperature superconducting (LTS) coils. The magnet was successfully charged without degradation and mainly operated at 400MHz (9.39T). Technical problems for the NMR magnet due to screening current in the REBCO coil were clarified and solved as follows: (i) A remarkable temporal drift of the central magnetic field was suppressed by a current sweep reversal method utilizing ∼10% of the peak current. (ii) A Z2 field error harmonic of the main coil cannot be compensated by an outer correction coil and therefore an additional ferromagnetic shim was used. (iii) Large tesseral harmonics emerged that could not be corrected by cryoshim coils. Due to those harmonics, the resolution and sensitivity of NMR spectra are ten-fold lower than those for a conventional LTS NMR magnet. As a result, a HSQC spectrum could be achieved for a protein sample, while a NOESY spectrum could not be obtained. An ultra-compact 1.2GHz NMR magnet could be realized if we effectively take advantage of REBCO conductors, although this will require further research to suppress the effect of the screening current.
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Affiliation(s)
- Y Yanagisawa
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan; Graduate School of Engineering, Chiba University, Chiba 236-8522, Japan
| | - R Piao
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan; Graduate School of Engineering, Chiba University, Chiba 236-8522, Japan
| | - S Iguchi
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan; Faculty of Science and Technology, Sophia University, Yotsuya 102-8554, Japan
| | - H Nakagome
- Graduate School of Engineering, Chiba University, Chiba 236-8522, Japan
| | - T Takao
- Faculty of Science and Technology, Sophia University, Yotsuya 102-8554, Japan
| | - K Kominato
- Japan Superconductor Technology, Inc, Kobe, Hyogo 651-2271, Japan
| | - M Hamada
- Japan Superconductor Technology, Inc, Kobe, Hyogo 651-2271, Japan
| | - S Matsumoto
- Superconducting Wire Unit, National Institute for Materials Science, Tsukuba 305-0003, Japan
| | - H Suematsu
- JEOL RESONANCE Inc., Akishima, Tokyo 196-8558, Japan
| | - X Jin
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan
| | - M Takahashi
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan
| | - T Yamazaki
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan
| | - H Maeda
- Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan.
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Jiang W, Jin YM, Lee J, Lee KI, Piao R, Han L, Shin JC, Jin RD, Cao T, Pan HY, Du X, Koh HJ. Quantitative trait loci for cold tolerance of rice recombinant inbred lines in low temperature environments. Mol Cells 2011; 32:579-87. [PMID: 22080374 PMCID: PMC3887680 DOI: 10.1007/s10059-011-0186-4] [Citation(s) in RCA: 19] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 09/25/2011] [Accepted: 09/28/2011] [Indexed: 01/30/2023] Open
Abstract
Low temperature is one of the major environmental stresses in rice cultivation in high-altitude and high-latitude regions. In this study, we cultivated a set of recombinant inbred lines (RIL) derived from Dasanbyeo (indica) / TR22183 (japonica) crosses in Yanji (high-latitude area), Kunming (high-altitude area), Chuncheon (cold water irrigation) and Suwon (normal) to evaluate the main effects of quantitative trait loci (QTL) and epistatic QTL (E-QTL) with regard to their interactions with environments for cold-related traits. Six QTLs for spikelet fertility (SF) were identified in three cold treatment locations. Among them, four QTLs on chromosomes 2, 7, 8, and 10 were validated by several near isogenic lines (NILs) under cold treatment in Chuncheon. A total of 57 QTLs and 76 E-QTLs for nine cold-related traits were identified as distributing on all 12 chromosomes; among them, 19 QTLs and E-QTLs showed significant interactions of QTLs and environments (QEIs). The total phenotypic variation explained by each trait ranged from 13.2 to 29.1% in QTLs, 10.6 to 29.0% in EQTLs, 2.2 to 8.8% in QEIs and 1.0% to 7.7% in E-QTL × environment interactions (E-QEIs). These results demonstrate that epistatic effects and QEIs are important properties of QTL parameters for cold tolerance at the reproductive stage. In order to develop cold tolerant varieties adaptable to wide-ranges of cold stress, a strategy facilitating marker-assisted selection (MAS) is being adopted to accumulate QTLs identified from different environments.
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Affiliation(s)
- Wenzhu Jiang
- College of Plant Science, Jilin University, Changchun, 130062, China
- These authors contributed equally to this work
| | - Yong-Mei Jin
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
- These authors contributed equally to this work
| | - Joohyun Lee
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Kang-Ie Lee
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Rihua Piao
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Longzhi Han
- Key Laboratory of Crop Germplasm Resources and Biotechnology, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jin-Chul Shin
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Korea
| | - Rong-De Jin
- Jilin Academy of Agricultural Sciences, Changchun 130124, China
| | - Tiehua Cao
- Jilin Academy of Agricultural Sciences, Changchun 130124, China
| | - Hong-Yu Pan
- Jilin Academy of Agricultural Sciences, Changchun 130124, China
| | - Xinglin Du
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Hee-Jong Koh
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
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Lestari P, Lee G, Ham TH, Reflinur, Woo MO, Piao R, Jiang W, Chu SH, Lee J, Koh HJ. Single nucleotide polymorphisms and haplotype diversity in rice sucrose synthase 3. ACTA ACUST UNITED AC 2011; 102:735-46. [PMID: 21914668 DOI: 10.1093/jhered/esr094] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rice sucrose synthase 3 (RSUS3) is expressed predominantly in rice seed endosperm and is thought to play an important role in starch filling during the milky stage of rice seed ripening. Because the genetic diversity of this locus is not known yet, the full sequence of RSUS3 from 43 rice varieties was amplified to examine the distribution of DNA polymorphisms. A total of 254 sequence variants, including SNPs and insertion/deletions, were successfully identified in the 7733 bp sequence that comprises the promoter, exons and introns, and 3' downstream nontranscribed region (NTR). Eleven haplotypes were distinguished among the 43 rice varieties based on nucleotide variation in the 3 defined regions (5' NTR, transcript, and 3' NTR). The promoter region showed evidence of a base change on a cis-element that might influence the functional role of the motif in seed-specific expression. The genetic diversity of the RSUS3 gene sequences in the rice germplasm used in this study appears to be the result of nonrandom processes. Analysis of polymorphism sites indicated that at least 11 recombinations have occurred, primarily in the transcribed region. This finding provides insight into the development of a cladistic approach for establishing future genetic association studies of the RSUS3 locus.
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Affiliation(s)
- Puji Lestari
- Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
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8
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Qiao Y, Piao R, Shi J, Lee SI, Jiang W, Kim BK, Lee J, Han L, Ma W, Koh HJ. Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.). Theor Appl Genet 2011; 122:1439-49. [PMID: 21318372 DOI: 10.1007/s00122-011-1543-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 01/19/2011] [Indexed: 05/18/2023]
Abstract
Architecture of the rice inflorescence, which is determined mainly by the morphology, number and length of primary and secondary inflorescence branches, is an important agronomical trait. In the current study, we characterized a novel dense and erect panicle (EP) mutant, dep3, derived from the Oryza sativa ssp. japonica cultivar Hwacheong treated with N-methyl-N-nitrosourea. The panicle of the dep3 mutant remained erect from flowering to full maturation, whereas the panicle of the wild type plant began to droop after flowering. The dep3 mutation also regulated other panicle characteristics, including panicle length, grain shape and grain number per panicle. Anatomical observations revealed that the dep3 mutant had more small vascular bundles and a thicker culm than wild type plants, explaining the EP phenotype. Genetic analysis indicated that the phenotype with the dense and EP was controlled by a single recessive gene, termed dep3. The DEP3 gene was identified as the candidate via a map-based cloning approach and was predicted to encode a patatin-like phospholipase A2 (PLA2) superfamily domain-containing protein. The mutant allele gene carried a 408 bp genomic deletion within LOC_Os06g46350, which included the last 47 bp coding region of the third exon and the first 361 bp of the 3'-untranslated region. Taken together, our results indicated that the patatin-like PLA2 might play a significant role in the formation of vascular bundles, and that the dep3 mutant may provide another EP resource for rice breeding programs.
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Affiliation(s)
- Yongli Qiao
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
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Jiang W, Lee J, Jin YM, Qiao Y, Piao R, Jang SM, Woo MO, Kwon SW, Liu X, Pan HY, Du X, Koh HJ. Identification of QTLs for seed germination capability after various storage periods using two RIL populations in rice. Mol Cells 2011; 31:385-92. [PMID: 21399992 PMCID: PMC3933968 DOI: 10.1007/s10059-011-0049-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/24/2011] [Accepted: 01/24/2011] [Indexed: 10/18/2022] Open
Abstract
Seed germination capability of rice is one of the important traits in the production and storage of seeds. Quantitative trait loci (QTL) associated with seed germination capability in various storage periods was identified using two sets of recombinant inbred lines (RILs) which derived from crosses between Milyang 23 and Tong 88-7 (MT-RILs) and between Dasanbyeo and TR22183 (DT-RILs). A total of five and three main additive effects (QTLs) associated with seed germination capability were identified in MT-RILs and DT-RILs, respectively. Among them, six QTLs were identified repeatedly in various seed storage periods designated as qMT-SGC5.1, qMT-SGC7.2, and qMT-SGC9.1 on chromosomes 5, 7, and 9 in MT-RILs, and qDT-SGC2.1, qDT-SGC3.1, and qDT-SGC9.1 on chromosomes 2, 3, and 9 in DT-RILs, respectively. The QTL on chromosome 9 was identified in both RIL populations under all three storage periods, explaining up to 40% of the phenotypic variation. Eight and eighteen pairs additive × additive epistatic effect (epistatic QTL) were identified in MT-RILs and DT-RILs, respectively. In addition, several near isogenic lines (NILs) were developed to confirm six repeatable QTL effects using controlled deterioration test (CDT). The identified QTLs will be further studied to elucidate the mechanisms controlling seed germination capability, which have important implications for long-term seed storage.
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Affiliation(s)
- Wenzhu Jiang
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Joohyun Lee
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Yong-Mei Jin
- School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea
| | - Yongli Qiao
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Rihua Piao
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Sun Mi Jang
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Mi-Ok Woo
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Soon-Wook Kwon
- Department of Agricultural Sciences, Korea National Open University, Seoul 110- 791, Korea
| | - Xianhu Liu
- Department of Agricultural Sciences, Yanbian University, Yanji 133000, China
| | - Hong-Yu Pan
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Xinglin Du
- College of Plant Science, Jilin University, Changchun 130062, China
| | - Hee-Jong Koh
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
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10
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Qiao Y, Lee SI, Piao R, Jiang W, Ham TH, Chin JH, Piao Z, Han L, Kang SY, Koh HJ. Fine mapping and candidate gene analysis of the floury endosperm gene, FLO(a), in rice. Mol Cells 2010; 29:167-74. [PMID: 20016946 DOI: 10.1007/s10059-010-0010-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/19/2009] [Accepted: 10/28/2009] [Indexed: 10/20/2022] Open
Abstract
In addition to its role as an energy source for plants, animals and humans, starch is also an environmentally friendly alternative to fossil fuels. In rice, the eating and cooking quality of the grain is determined by its starch properties. The floury endosperm of rice has been explored as an agronomical trait in breeding and genetics studies. In the present study, we characterized a floury endosperm mutant, flo(a), derived from treatment of Oryza sativa ssp. japonica cultivar Hwacheong with MNU. The innermost endosperm of the flo(a) mutant exhibited floury characteristics while the outer layer of the endosperm appeared normal. Starch granules in the flo(a) mutant formed a loosely-packed crystalline structure and X-ray diffraction revealed that the overall crystallinity of the starch was decreased compared to wild-type. The FLO(a) gene was isolated via a map-based cloning approach and predicted to encode the tetratricopeptide repeat domain-containing protein, OsTPR. Three mutant alleles contain a nucleotide substitution that generated one stop codon or one splice site, respectively, which presumably disrupts the interaction of the functionally conserved TPR motifs. Taken together, our map-based cloning approach pinpointed an OsTPR as a strong candidate of FLO(a), and the proteins that contain TPR motifs might play a significant role in rice starch biosynthetic pathways.
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Affiliation(s)
- Yongli Qiao
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea
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11
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Qiao Y, Jiang W, Lee J, Park B, Choi MS, Piao R, Woo MO, Roh JH, Han L, Paek NC, Seo HS, Koh HJ. SPL28 encodes a clathrin-associated adaptor protein complex 1, medium subunit micro 1 (AP1M1) and is responsible for spotted leaf and early senescence in rice (Oryza sativa). New Phytol 2010; 185:258-74. [PMID: 19825016 DOI: 10.1111/j.1469-8137.2009.03047.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To expand our understanding of cell death in plant defense responses, we isolated a novel rice (Oryza sativa) spotted leaf mutant (spl28) that displays a lesion mimic phenotype in the absence of pathogen attack through treatment of Hwacheongbyeo (an elite Korean japonica cultivar) with N-methyl-N-nitrosourea (MNU). Early stage development of the spl28 mutant was normal. However, after flowering, spl28 mutants exhibited a significant decrease in chlorophyll content, soluble protein content, and photosystem II efficiency, and high concentrations of reactive oxygen species (ROS), phytoalexin, callose, and autofluorescent phenolic compounds that localized in or around the lesions. The spl28 mutant also exhibited significantly enhanced resistance to rice blast and bacterial blight. Using a map-based cloning approach, we determined that SPL28 encodes a clathrin-associated adaptor protein complex 1, medium subunit micro 1 (AP1M1), which is involved in the post-Golgi trafficking pathway. A green fluorescent protein (GFP) fusion protein of SPL28 (SPL28::GFP) localized to the Golgi apparatus, and expression of SPL28 complemented the membrane trafficking defect of apm1-1 Delta yeast mutants. SPL28 was ubiquitously expressed and contained a highly conserved adaptor complex medium subunit (ACMS) family domain. SPL28 appears to be involved in the regulation of vesicular trafficking, and SPL28 dysfunction causes the formation of hypersensitive response (HR)-like lesions, leading to the initiation of leaf senescence.
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Affiliation(s)
- Yongli Qiao
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Republic of Korea
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12
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Piao R, Jiang W, Ham TH, Choi MS, Qiao Y, Chu SH, Park JH, Woo MO, Jin Z, An G, Lee J, Koh HJ. Map-based cloning of the ERECT PANICLE 3 gene in rice. Theor Appl Genet 2009; 119:1497-506. [PMID: 19756471 DOI: 10.1007/s00122-009-1151-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 08/30/2009] [Indexed: 05/25/2023]
Abstract
Panicle architecture in rice can have a strong influence on yield. Using N-methyl-N-nitrosourea mutagenesis, we isolated an erect panicle mutant, Hep, from Hwasunchalbyeo, a glutinous japonica rice cultivar. Genetic analysis revealed that the erect panicle phenotype was controlled by a single recessive mutation designated erect panicle 3 (ep3). Genetic mapping revealed that the ep3 mutation was located on the short arm of chromosome 2 in a 0.1 cM region delimited by the STS markers STS5803-5 and STS5803-7. The ep3 locus corresponded to 46.8 kb region and contained six candidate genes. Comparison of the DNA sequences of the candidate genes from wild-type and erect panicle plants revealed a single base-pair change in the second exon of LOC_Os02g15950, which is predicted to result in a nonsense mutation. LOC_Os02g15950 encodes a putative F-box protein containing 515 amino acids and is expressed throughout the plant during all growth stages. A line carrying a T-DNA insertion in LOC_ Os02g15950 was obtained and shown to have the same phenotype as the ep3 mutant, thus confirming the identification of LOC_Os02g15950 as the ERECT PANICLE 3 (EP3) gene. The ep3 mutation causes a significant increase in the number of small vascular bundles as well as the thickness of parenchyma in the peduncle, which results in the erect panicle phenotype.
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Affiliation(s)
- Rihua Piao
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
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13
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Li Y, Guan R, Liu Z, Ma Y, Wang L, Li L, Lin F, Luan W, Chen P, Yan Z, Guan Y, Zhu L, Ning X, Smulders MJM, Li W, Piao R, Cui Y, Yu Z, Guan M, Chang R, Hou A, Shi A, Zhang B, Zhu S, Qiu L. Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet 2008; 117:857-71. [PMID: 18587557 DOI: 10.1007/s00122-008-0825-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 06/08/2008] [Indexed: 05/10/2023]
Abstract
The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic differentiation in order to provide useful information for effective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly significant pairwise Fst values and was generally in accordance with differences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5 degrees N, 105.4 and 122.2 degrees E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the first molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from different loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, fixed in homozygous self-fertilizing landraces.
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Affiliation(s)
- Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm and Biotechnology (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
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14
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Zhao L, Li H, Jiang Y, Piao R, Li P, Gu J. Determination of Ranolazine in Human Plasma by Liquid Chromatographic--Tandem Mass Spectrometric Assay. J Chromatogr Sci 2008; 46:697-700. [DOI: 10.1093/chromsci/46.8.697] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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15
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Qiao Y, Jiang W, Rahman ML, Chu SH, Piao R, Han L, Koh HJ. Comparison of molecular linkage maps and QTLs for morphological traits in two reciprocal backcross populations of rice. Mol Cells 2008; 25:417-27. [PMID: 18443414] [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
Comparison of maps and QTLs between populations may provide us with a better understanding of molecular maps and the inheritance of traits. We developed and used two reciprocal BC1F1 populations, IP/DS//IP and IP/DS//DS, for QTL analysis. DS (Dasanbyeo) is a Korean tongil-type cultivar (derived from an indica x japonica cross and similar to indica in its genetic make-up) and IP (Ilpumbyeo) is a Korean japonica cultivar. We constructed two molecular linkage maps corresponding to each backcross population using 196 markers for each map. The length of each chromosome was longer in the IP/DS//IP population than in the IP/DS//DS population, indicating that more recombinants were produced in the IP/DS//IP population. Distorted segregation was observed for 44 and 19 marker loci for the IP/DS//IP and IP/DS//DS populations, respectively; these were mostly skewed in favor of the indica alleles. A total of 36 main effect QTLs (M-QTLs) and 15 digenic epistatic interactions (E-QTLs) were detected for the seven traits investigated. The phenotypic variation explained (PVE) by M-QTLs ranged from 3.4% to 88.2%. Total PVE of the M-QTLs for each trait was significantly higher than that of the E-QTLs. The total number of M-QTLs identified in the IP/DS//IP population was higher than in the IP/DS//DS population. However, the total PVE by the M-QTLs and E-QTLs together for each trait was similar in the two populations, suggesting that the two BC1F1 populations are equally useful for QTL analysis. Maps and QTLs in the two populations were compared. Eleven new QTLs were identified for SN, SF, GL, and GW in this study, and they will be valuable in marker-assisted selection, particularly for improving grain traits in tongil-type varieties.
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Affiliation(s)
- Yongli Qiao
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
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16
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Jiang W, Chu SH, Piao R, Chin JH, Jin YM, Lee J, Qiao Y, Han L, Piao Z, Koh HJ. Fine mapping and candidate gene analysis of hwh1 and hwh2, a set of complementary genes controlling hybrid breakdown in rice. Theor Appl Genet 2008; 116:1117-1127. [PMID: 18335199 DOI: 10.1007/s00122-008-0740-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2007] [Accepted: 02/25/2008] [Indexed: 05/26/2023]
Abstract
Hybrid breakdown (HB), a phenomenon of reduced viability or fertility accompanied with retarded growth in hybrid progenies, often arises in the offspring of intersubspecific hybrids between indica and japonica in rice. We detected HB plants in F8 recombinant inbred lines derived from the cross between an indica variety, Milyang 23, and a japonica variety, Tong 88-7. HB plants showed retarded growth, with fewer tillers and spikelets. Genetic analysis revealed that HB was controlled by the complementary action of two recessive genes, hwh1 and hwh2, originating from each of both parents, which were fine-mapped on the short arm of chromosome 2 and on the near centromere region of the long arm of chromosome 11, respectively. A comparison of the sequences of candidate genes among both parents and HB plants revealed that hwh1 encoded a putative glucose-methanol-choline oxidoreductase with one amino acid change compared to Hwh1 and that hwh2 probably encoded a putative hexose transporter with a six amino acid insertion compared to Hwh2. Investigation of the distribution of these alleles among 54 japonica and indica cultivars using candidate gene-based markers suggested that the two loci might be involved in developing reproductive barriers between two subspecies.
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Affiliation(s)
- Wenzhu Jiang
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea
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17
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Woo MO, Ham TH, Ji HS, Choi MS, Jiang W, Chu SH, Piao R, Chin JH, Kim JA, Park BS, Seo HS, Jwa NS, McCouch S, Koh HJ. Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.). Plant J 2008; 54:190-204. [PMID: 18182026 PMCID: PMC2327258 DOI: 10.1111/j.1365-313x.2008.03405.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 12/04/2007] [Indexed: 05/17/2023]
Abstract
A rice genic male-sterility gene ms-h is recessive and has a pleiotropic effect on the chalky endosperm. After fine mapping, nucleotide sequencing analysis of the ms-h gene revealed a single nucleotide substitution at the 3'-splice junction of the 14th intron of the UDP-glucose pyrophosphorylase 1 (UGPase1; EC2.7.7.9) gene, which causes the expression of two mature transcripts with abnormal sizes caused by the aberrant splicing. An in vitro functional assay showed that both proteins encoded by the two abnormal transcripts have no UGPase activity. The suppression of UGPase by the introduction of a UGPase1-RNAi construct in wild-type plants nearly eliminated seed set because of the male defect, with developmental retardation similar to the ms-h mutant phenotype, whereas overexpression of UGPase1 in ms-h mutant plants restored male fertility and the transformants produced T(1) seeds that segregated into normal and chalky endosperms. In addition, both phenotypes were co-segregated with the UGPase1 transgene in segregating T(1) plants, which demonstrates that UGPase1 has functional roles in both male sterility and the development of a chalky endosperm. Our results suggest that UGPase1 plays a key role in pollen development as well as seed carbohydrate metabolism.
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Affiliation(s)
- Mi-Ok Woo
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
| | - Tae-Ho Ham
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
| | - Hyeon-So Ji
- National Institute of Agricultural BiotechnologyRDA, Suwon 441-707, Korea
| | - Min-Seon Choi
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
| | - Wenzhu Jiang
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
| | - Sang-Ho Chu
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
| | - Rihua Piao
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
| | | | - Jung-A Kim
- Department of Molecular Biology, College of Natural Science, Sejong UniversitySeoul 143-747, Korea
| | - Bong Soo Park
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
| | - Hak Soo Seo
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
| | - Nam-Soo Jwa
- Department of Molecular Biology, College of Natural Science, Sejong UniversitySeoul 143-747, Korea
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell UniversityIthaca, NY 14853-1901, USA
| | - Hee-Jong Koh
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul 151-921, Korea
- For correspondence (fax +82 2 873 2056; e-mail )
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18
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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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Maeng JY, Won YJ, Piao R, Cho YI, Jiang W, Chin JH, Koh HJ. Molecular mapping of a gene 'ld(t)' controlling cleistogamy in rice. Theor Appl Genet 2006; 112:1429-33. [PMID: 16525838 DOI: 10.1007/s00122-006-0244-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 02/13/2006] [Indexed: 05/07/2023]
Abstract
Cleistogamy is the self-pollination within closed spikelets and is expected to be a useful genetic tool for prevention of possible gene transfer in transgenic crops, for maintenance of genetic purity in autogamous crops, and for increased tolerance to biotic and abiotic stresses. Mapping of the gene ld(t), which is responsible for lack of lodicules inside spikelets and causes cleistogamy, was carried out using F2 and F3 populations derived from a cleistogamous (CL) mutant CL-SNU x Milyang 23 cross. A number of STS markers along chromosomes were developed and bulked segregant analysis was adopted for preliminary mapping. The results showed that the ld(t) was located at the end region of chromosome 1L, flanked by S01178b (an STS marker developed for the locus at 178 cM based on the rice genetic map reported by Japanese Rice Genome Project) at 0.8 cM and co-segregated with S01181a and S01181b (an STS marker developed for the locus at 181 cM).
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Affiliation(s)
- Ji-Young Maeng
- College of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Korea
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