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Hamisu A, Koul B, Arukha AP, Al Nadhari S, Rabbee MF. Evaluation of the Impact of Chemical Mutagens on the Phenological and Biochemical Characteristics of Two Varieties of Soybean ( Glycine max L.). Life (Basel) 2024; 14:909. [PMID: 39063662 PMCID: PMC11277911 DOI: 10.3390/life14070909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/05/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Mutagenic effectiveness and efficiency are the most important factors determining the success of mutation breeding, a coherent tool for quickly enhancing diversity in crops. This study was carried out at Lovely Professional University's agricultural research farm in Punjab, India, during the year 2023. The experimental design followed a randomized complete block design (RCBD) with three replications. The experiment aimed to assess the effect of three chemical mutagens, sodium azide (SA), ethyl methyl sulphonates (EMSs), and methyl methane sulfonate (MMS), at three different concentrations (0.2%, 0.4%, and 0.6%), in SL958 and SL744 soybean varieties to select the mutant exhibiting the highest yield. The data were collected and analysed using a two-way ANOVA test through SPSS software (version 22), and the means were separated using Duncan's multiple range test (DMRT) at the 5% level of significance. Between the two varieties, the highest seed germination percentage (76.0% seedlings/plot) was recorded in SL958 (0.4% SA), while the lowest (30.33% seedlings/plot) was observed in 0.6% MMS as compared to the control (53% and 76% in SL744 and SL958 at 10 days after sowing, respectively). Several weeks after sowing, the average plant height was observed to be higher (37.84 ± 1.32 cm) in SL958 (0.4% SA) and lower (20.58 ± 0.30 cm) in SL744 (0.6% SA), as compared to the controls (SL958: 26.09 ± 0.62 cm and SL744: 27.48 ± 0.74 cm). The average leaf count was the highest (234.33 ± 3.09 tetrafoliate leaves/plant) in SL958 (0.4% SA) while it was the lowest (87 leaves/plant) in 0.6% MMS as compared to the control (SL744 180.00 ± 1.63 and SL958 160.73 ± 1.05). The highest total leaf areas recorded in the SL958 and SL744 M1plants were 3625.8 ± 1.43 cm2 and 2311.03 ± 3.65 cm2, respectively. Seeds of the SL958 variety treated with 0.4% SA resulted in the development of tetrafoliate leaves with a broad leaf base and the maximum yield (277.55 ± 1.37 pods/plant) compared to the narrow pentafoliate leaves obtained through the treatment with EMS. Meanwhile, in the SL744 variety, the same treatment led to tetrafoliate leaves with a comparatively lower yield of 206.54 ± 23.47 pods/plant as compared to the control (SL744 164.33 ± 8.58 and SL958 229.86 ± 0.96). The highest protein content (47.04 ± 0.87% TSP) was recorded in the SL958 (0.4% SA) M2 seeds followed by a content of 46.14 ± 0.64% TSP in the SL744 (0.4% SA) M2 seeds, whereas the lowest content (38.13 ± 0.81% TSP) was found in SL958 (0.6% MMS). Similar observations were recorded for the lipid and fibre content. The 0.4% SA treatment in SL958 proved to be efficient in generating the highest leaf area (tetrafoliate leaves) and a reasonable yield of M1 (the first generation after mutation) plants.
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Affiliation(s)
- Anas Hamisu
- Department of Botany, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Bhupendra Koul
- Department of Botany, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Ananta Prasad Arukha
- Department of Nephrology and Hypertension, Mayo Medical Sciences, Rochester, MN 55902, USA;
| | - Saleh Al Nadhari
- Deanship of Scientific Research, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Muhammad Fazle Rabbee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
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Rice TCD8 Encoding a Multi-Domain GTPase Is Crucial for Chloroplast Development of Early Leaf Stage at Low Temperatures. BIOLOGY 2022; 11:biology11121738. [PMID: 36552248 PMCID: PMC9774597 DOI: 10.3390/biology11121738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022]
Abstract
The multi-domain GTPase (MnmE) is conservative from bacteria to human and participates in tRNA modified synthesis. However, our understanding of how the MnmE is involved in plant chloroplast development is scarce, let alone in rice. A novel rice mutant, thermo-sensitive chlorophyll-deficient mutant 8 (tcd8) was identified in this study, which apparently presented an albino phenotype at 20 °C but a normal green over 24 °C, coincided with chloroplast development and chlorophyll content. Map-based cloning and complementary test revealed the TCD8 encoded a multi-domain GTPase localized in chloroplasts. In addition, the disturbance of TCD8 suppressed the transcripts of certain chloroplast-related genes at low temperature, although the genes were recoverable to nearly normal levels at high temperature (32 °C), indicating that TCD8 governs chloroplast development at low temperature. The multi-domain GTPase gene in rice is first reported in this study, which endorses the importance in exploring chloroplast development in rice.
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Hasan S, Furtado A, Henry R. Gene Expression in the Developing Seed of Wild and Domesticated Rice. Int J Mol Sci 2022; 23:13351. [PMID: 36362135 PMCID: PMC9658725 DOI: 10.3390/ijms232113351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 01/06/2024] Open
Abstract
The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (Oryza sativa ssp. japonica var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (Oryza meridionalis and Oryza rufipogon type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (Bh4) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value.
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Affiliation(s)
- Sharmin Hasan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia 4072, Australia
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Lin N, Gao Y, Zhou Q, Ping X, Li J, Liu L, Yin J. Genetic mapping and physiological analysis of chlorophyll-deficient mutant in Brassica napus L. BMC PLANT BIOLOGY 2022; 22:244. [PMID: 35585493 PMCID: PMC9115954 DOI: 10.1186/s12870-022-03630-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Leaf color mutants have reduced photosynthetic efficiency, which has severely negative impacts on crop growth and economic product yield. There are different chlorophyll mutants in Arabidopsis and crops that can be used for genetic control and molecular mechanism studies of chlorophyll biosynthesis, chloroplast development and photoefficiency. Chlorophyll mutants in Brassica napus are mostly used for mapping and location research but are rarely used for physiological research. The chlorophyll-deficient mutant in this experiment were both genetically mapped and physiologically analyzed. RESULTS In this study, yellow leaf mutant of Brassica napus L. mutated by ethyl methyl sulfone (EMS) had significantly lower chlorophyll a, b and carotenoid contents than the wild type, and the net photosynthetic efficiency, stomatal conductance and transpiration rate were all significantly reduced. The mutant had sparse chloroplast distribution and weak autofluorescence. The granule stacks were reduced, and the shape was extremely irregular, with more broken stromal lamella. Transcriptome data analysis enriched the differentially expressed genes mainly in phenylpropane and sugar metabolism. The mutant was mapped to a 2.72 Mb region on A01 by using BSA-Seq, and the region was validated by SSR markers. CONCLUSIONS The mutant chlorophyll content and photosynthetic efficiency were significantly reduced compared with those of the wild type. Abnormal chloroplasts and thylakoids less connected to the stroma lamella appeared in the mutant. This work on the mutant will facilitate the process of cloning the BnaA01.cd gene and provide more genetic and physiological information concerning chloroplast development in Brassica napus.
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Affiliation(s)
- Na Lin
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
| | - Yumin Gao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
| | - Qingyuan Zhou
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
| | - Xiaoke Ping
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
- Academy of Agricultural Sciences, Southwest University, Tiansheng Rd2#, Beibei, Chongqing, 400715, PR China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
- Academy of Agricultural Sciences, Southwest University, Tiansheng Rd2#, Beibei, Chongqing, 400715, PR China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
- Academy of Agricultural Sciences, Southwest University, Tiansheng Rd2#, Beibei, Chongqing, 400715, PR China
| | - Jiaming Yin
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China.
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Yoon J, Cho L, Kim S, Tun W, Peng X, Pasriga R, Moon S, Hong W, Ji H, Jung K, Jeon J, An G. CTP synthase is essential for early endosperm development by regulating nuclei spacing. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2177-2191. [PMID: 34058048 PMCID: PMC8541778 DOI: 10.1111/pbi.13644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/04/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Cereal grain endosperms are an important source of human nutrition. Nuclear division in early endosperm development plays a major role in determining seed size; however, this development is not well understood. We identified the rice mutant endospermless 2 (enl2), which shows defects in the early stages of endosperm development. These phenotypes arise from mutations in OsCTPS1 that encodes a cytidine triphosphate synthase (CTPS). Both wild-type and mutant endosperms were normal at 8 h after pollination (HAP). In contrast, at 24 HAP, enl2 endosperm had approximately 10-16 clumped nuclei while wild-type nuclei had increased in number and migrated to the endosperm periphery. Staining of microtubules in endosperm at 24 HAP revealed that wild-type nuclei were evenly distributed by microtubules while the enl2-2 nuclei were tightly packed due to their reduction in microtubule association. In addition, OsCTPS1 interacts with tubulins; thus, these observations suggest that OsCTPS1 may be involved in microtubule formation. OsCTPS1 transiently formed macromolecular structures in the endosperm during early developmental stages, further supporting the idea that OsCTPS1 may function as a structural component during endosperm development. Finally, overexpression of OsCTPS1 increased seed weight by promoting endosperm nuclear division, suggesting that this trait could be used to increase grain yield.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Lae‐Hyeon Cho
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Sung‐Ryul Kim
- Gene Identification and Validation GroupGenetic Design and Validation UnitInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Win Tun
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Xin Peng
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Sunok Moon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Woo‐Jong Hong
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Hyeonso Ji
- National Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Ki‐Hong Jung
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Jong‐Seong Jeon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
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Jung YJ, Lee HJ, Yu J, Bae S, Cho YG, Kang KK. Transcriptomic and physiological analysis of OsCAO1 knockout lines using the CRISPR/Cas9 system in rice. PLANT CELL REPORTS 2021; 40:1013-1024. [PMID: 32980909 DOI: 10.1007/s00299-020-02607-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
The altered rice leaf color based on the knockout of CAO1 gene generated using CRISPR/Cas9 technology plays important roles in chlorophyll degradation and ROS scavenging to regulate both natural and induced senescence in rice. Rice chlorophyllide a oxygenase (OsCAO1), identified as the chlorophyll b synthesis under light condition, plays a critical role in regulating rice plant photosynthesis. In this study, the development of edited lines with pale green leaves by knockout of OsCAO1 gene known as a chlorophyll synthesis process is reported. Eighty-one genetically edited lines out of 181 T0 plants were generated through CRISPR/Cas9 system. The edited lines have short narrow flag leaves and pale green leaves compared with wild-type 'Dongjin' plants (WT). Additionally, edited lines have lower chlorophyll b and carotenoid contents both at seedling and mature stages. A transcriptome analysis identified 580 up-regulated and 206 downregulated genes in the edited lines. The differentially expressed genes (DEGs) involved in chlorophyll biosynthesis, magnesium chelatase subunit (CHLH), and glutamate-1-semialdehyde2, 1-aminomutase (GSA) metabolism decreased significantly. Meanwhile, the gel consistency (GC) levels of rice grains, chalkiness ratios and chalkiness degrees (CD) decreased in the edited lines. Thus, knockout of OsCAO1 influenced growth period, leaf development and grain quality characters of rice. Overall, the result suggests that OsCAO1 also plays important roles in chlorophyll degradation and ROS scavenging to regulate both natural and induced rice senescence.
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Affiliation(s)
- Yu Jin Jung
- Division of Horticultural Biotechnology, Hankyong National University, Anseong, 17579, South Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong, 17579, South Korea
| | - Hyo Ju Lee
- Division of Horticultural Biotechnology, Hankyong National University, Anseong, 17579, South Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
| | - Yong-Gu Cho
- Department of Crop Science, Chungbuk National University, Cheongju, 28644, South Korea
| | - Kwon Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong, 17579, South Korea.
- Institute of Genetic Engineering, Hankyong National University, Anseong, 17579, South Korea.
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Lin T, Zhou R, Bi B, Song L, Chai M, Wang Q, Song G. Analysis of a radiation-induced dwarf mutant of a warm-season turf grass reveals potential mechanisms involved in the dwarfing mutant. Sci Rep 2020; 10:18913. [PMID: 33144613 PMCID: PMC7609746 DOI: 10.1038/s41598-020-75421-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/14/2020] [Indexed: 11/09/2022] Open
Abstract
Zoysia matrella [L.] Merr. is a widely cultivated warm-season turf grass in subtropical and tropical areas. Dwarf varieties of Z. matrella are attractive to growers because they often reduce lawn mowing frequencies. In this study, we describe a dwarf mutant of Z. matrella induced from the 60Co-γ-irradiated calluses. We conducted morphological test and physiological, biochemical and transcriptional analyses to reveal the dwarfing mechanism in the mutant. Phenotypically, the dwarf mutant showed shorter stems, wider leaves, lower canopy height, and a darker green color than the wild type (WT) control under the greenhouse conditions. Physiologically, we found that the phenotypic changes of the dwarf mutant were associated with the physiological responses in catalase, guaiacol peroxidase, superoxide dismutase, soluble protein, lignin, chlorophyll, and electric conductivity. Of the four endogenous hormones measured in leaves, both indole-3-acetic acid and abscisic acid contents were decreased in the mutant, whereas the contents of gibberellin and brassinosteroid showed no difference between the mutant and the WT control. A transcriptomic comparison between the dwarf mutant and the WT leaves revealed 360 differentially-expressed genes (DEGs), including 62 up-regulated and 298 down-regulated unigenes. The major DEGs related to auxin transportation (e.g., PIN-FORMED1) and cell wall development (i.e., CELLULOSE SYNTHASE1) and expansin homologous genes were all down-regulated, indicating their potential contribution to the phenotypic changes observed in the dwarf mutant. Overall, the results provide information to facilitate a better understanding of the dwarfing mechanism in grasses at physiological and transcript levels. In addition, the results suggest that manipulation of auxin biosynthetic pathway genes can be an effective approach for dwarfing breeding of turf grasses.
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Affiliation(s)
- Tianyi Lin
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ren Zhou
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bo Bi
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Liangyuan Song
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mingliang Chai
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Qiaomei Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Guoqing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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Subudhi PK, Garcia RS, Coronejo S, De Leon TB. A Novel Mutation of the NARROW LEAF 1 Gene Adversely Affects Plant Architecture in Rice ( Oryza sativa L.). Int J Mol Sci 2020; 21:ijms21218106. [PMID: 33143090 PMCID: PMC7672626 DOI: 10.3390/ijms21218106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/25/2020] [Accepted: 10/26/2020] [Indexed: 11/17/2022] Open
Abstract
Plant architecture is critical for enhancing the adaptability and productivity of crop plants. Mutants with an altered plant architecture allow researchers to elucidate the genetic network and the underlying mechanisms. In this study, we characterized a novel nal1 rice mutant with short height, small panicle, and narrow and thick deep green leaves that was identified from a cross between a rice cultivar and a weedy rice accession. Bulked segregant analysis coupled with genome re-sequencing and cosegregation analysis revealed that the overall mutant phenotype was caused by a 1395-bp deletion spanning over the last two exons including the transcriptional end site of the nal1 gene. This deletion resulted in chimeric transcripts involving nal1 and the adjacent gene, which were validated by a reference-guided assembly of transcripts followed by PCR amplification. A comparative transcriptome analysis of the mutant and the wild-type rice revealed 263 differentially expressed genes involved in cell division, cell expansion, photosynthesis, reproduction, and gibberellin (GA) and brassinosteroids (BR) signaling pathways, suggesting the important regulatory role of nal1. Our study indicated that nal1 controls plant architecture through the regulation of genes involved in the photosynthetic apparatus, cell cycle, and GA and BR signaling pathways.
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Affiliation(s)
- Prasanta K. Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (R.S.G.); (S.C.)
- Correspondence: ; Tel.: +1-225-578-1303
| | - Richard S. Garcia
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (R.S.G.); (S.C.)
| | - Sapphire Coronejo
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (R.S.G.); (S.C.)
| | - Teresa B. De Leon
- California Cooperative Rice Research Foundation, Inc., Biggs, CA 95917, USA;
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Zafar SA, Hameed A, Ashraf M, Khan AS, Qamar ZU, Li X, Siddique KHM. Agronomic, physiological and molecular characterisation of rice mutants revealed the key role of reactive oxygen species and catalase in high-temperature stress tolerance. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:440-453. [PMID: 32209204 DOI: 10.1071/fp19246] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 12/09/2019] [Indexed: 05/20/2023]
Abstract
Climatic variations have increased the occurrence of heat stress during critical growth stages, which negatively affects grain yield in rice. Plants adapt to harsh environments, and particularly high-temperature stress, by regulating their physiological and biochemical processes, which are key tolerance mechanisms. The identification of heat-tolerant rice genotypes and reliable selection indices are crucial for rice improvement programs. Here, we evaluated the response of a rice mutant population for high-temperature stress at the seedling and reproductive stages based on agronomic, physiological and molecular indices. Estimates of variance components revealed significant differences (P < 0.001) among genotypes, treatments and their interactions for almost all traits. The principal component analysis showed significant diversity among genotypes and traits under high-temperature stress. The mutant HTT-121 was identified as the most heat-tolerant mutant with higher grain yield, panicle fertility, cell membrane thermo-stability (CMTS) and antioxidant enzyme levels under heat stress. Various seedling-based morpho-physiological traits (leaf fresh weight, relative water contents, malondialdehyde, CMTS) and biochemical traits (superoxide dismutase, catalase and hydrogen peroxide) explained variations in grain yield that could be used as selection indices for heat tolerance in rice during early growth. Notably, heat-sensitive mutants accumulated reactive oxygen species, reduced catalase activity and upregulated OsSRFP1 expression under heat stress, suggesting their key roles in regulating heat tolerance in rice. The heat-tolerant mutants identified in this study could be used in breeding programs and to develop mapping populations to unravel the underlying genetic architecture for heat-stress adaptability.
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Affiliation(s)
- Syed Adeel Zafar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan; and Nuclear Institute for Agriculture and Biology (NIAB), PO Box 128, Faisalabad, Pakistan; and National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Amjad Hameed
- Nuclear Institute for Agriculture and Biology (NIAB), PO Box 128, Faisalabad, Pakistan; and Corresponding authors. ;
| | - Muhammad Ashraf
- Nuclear Institute for Agriculture and Biology (NIAB), PO Box 128, Faisalabad, Pakistan
| | - Abdus Salam Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zia-Ul- Qamar
- Nuclear Institute for Agriculture and Biology (NIAB), PO Box 128, Faisalabad, Pakistan
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; and Corresponding authors. ;
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Zhang K, Mu Y, Li W, Shan X, Wang N, Feng H. Identification of two recessive etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis). BMC PLANT BIOLOGY 2020; 20:68. [PMID: 32041529 PMCID: PMC7011377 DOI: 10.1186/s12870-020-2271-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/29/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Leaf color is a major agronomic trait, which has a strong influence on crop yields. Isolating leaf color mutants can represent valuable materials for research in chlorophyll (Chl) biosynthesis and metabolism regulation. RESULTS In this study, we identified a stably inherited yellow leaf mutant derived from 'Huaguan' pakchoi variety via isolated microspore culture and designated as pylm. This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Genetic analysis revealed that two recessive nuclear genes, named py1 and py2, are responsible for the etiolation phenotype. Bulked segregant RNA sequencing (BSR-Seq) showed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism (SNP) of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1520 F3:4 yellow-colored individuals co-segregated with py1. For py2, 1860 recessive homozygous F3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One SNP of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to quantitative real-time polymerase chain reaction (qRT-PCR), BraA07001774 was downregulated in pylm. CONCLUSIONS Our study identified a Chl deficiency mutant pylm in pakchoi. Two recessive nuclear genes named py1 and py2 had a significant effect on etiolation. Candidate genes regulating etiolation were identified as BraA09004189 and BraA07001774, respectively. These findings will elucidate chlorophyll metabolism and the molecular mechanisms of the gene interactions controlling pakchoi etiolation.
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Affiliation(s)
- Kun Zhang
- College of Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Yu Mu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Weijia Li
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Xiaofei Shan
- College of Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Nan Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
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Ali Z, Raza Q, Atif RM, Aslam U, Ajmal M, Chung G. Genetic and Molecular Control of Floral Organ Identity in Cereals. Int J Mol Sci 2019; 20:E2743. [PMID: 31167420 PMCID: PMC6600504 DOI: 10.3390/ijms20112743] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals.
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Affiliation(s)
- Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan 66000, Pakistan.
| | - Qasim Raza
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku 39020, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Usman Aslam
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Ajmal
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea.
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Fast mapping of a chlorophyll b synthesis-deficiency gene in barley (Hordeum vulgare L.) via bulked-segregant analysis with reduced-representation sequencing. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Descalsota-Empleo GI, Noraziyah AAS, Navea IP, Chung C, Dwiyanti MS, Labios RJD, Ikmal AM, Juanillas VM, Inabangan-Asilo MA, Amparado A, Reinke R, Cruz CMV, Chin JH, Swamy BPM. Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice. Genes (Basel) 2019; 10:E30. [PMID: 30626141 PMCID: PMC6356647 DOI: 10.3390/genes10010030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 11/16/2022] Open
Abstract
Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.
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Affiliation(s)
- Gwen Iris Descalsota-Empleo
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- University of the Southern Mindanao, Kabacan, Cotabato 9407, Philippines.
| | | | - Ian Paul Navea
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- Nousbo Corp. #4-107, 89 Seohoro, Gwonsun, Suwon 16614, Gyeonggi, Korea.
| | - Chongtae Chung
- Chungcheongnam-do Agricultural Research and Extension Services, 167, Chusa-ro, Shinam-myeon, Yesan-gun 32418, Chungcheongnam-do, Korea.
| | - Maria Stefanie Dwiyanti
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- Applied Plant Genome Laboratory, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan.
| | | | - Asmuni Mohd Ikmal
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
| | | | | | - Amery Amparado
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
| | - Russell Reinke
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
| | | | - Joong Hyoun Chin
- Department of Integrative Bio-Industrial Engineering, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea.
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Lin D, Zheng K, Liu Z, Li Z, Teng S, Xu J, Dong Y. Rice TCM1 Encoding a Component of the TAC Complex is Required for Chloroplast Development under Cold Stress. THE PLANT GENOME 2018; 11:160065. [PMID: 29505628 DOI: 10.3835/plantgenome2016.07.0065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transcriptionally active chromosome (TAC) is a component of protein-DNA complexes with RNA polymerase activity, expressed in the plastid. However, the function of rice TAC proteins is still poorly understood. In this paper, we first report the identification of a new rice ( L.) mutant () in the gene encoding TAC. The mutant displayed an albino phenotype and malformed chloroplasts before the three-leaf stage when grown at low temperatures (20°C) and a normal phenotype at higher temperatures (>28°C). Map-based cloning revealed that encodes a novel chloroplast-targeted TAC protein in rice. In addition, the transcript levels of all examined plastid-encoded polymerase (PEP)-dependent genes were clearly downregulated in mutants at low temperatures, although partially recovering levels were obtained at high temperatures, comparable to wild-type plants. Furthermore, the transcripts were ubiquitously expressed in all examined tissues, with high expression levels in green tissues. The data suggest that the rice nuclear-encoded TAC protein TCM1 is essential for proper chloroplast development and maintaining PEP activity under cold stress.
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Wang WJ, Zheng KL, Gong XD, Xu JL, Huang JR, Lin DZ, Dong YJ. The rice TCD11 encoding plastid ribosomal protein S6 is essential for chloroplast development at low temperature. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 259:1-11. [PMID: 28483049 DOI: 10.1016/j.plantsci.2017.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 05/20/2023]
Abstract
Plastid ribosome proteins (PRPs) are important components for chloroplast biogenesis and early chloroplast development. Although it has been known that chloroplast ribosomes are similar to bacterial ones, the precise molecular function of ribosomal proteins remains to be elucidated in rice. Here, we identified a novel rice mutant, designated tcd11 (thermo-sensitive chlorophyll-deficient mutant 11), characterized by the albino phenotype until it died at 20°C, while displaying normal phenotype at 32°C. The alteration of leaf color in tcd11 mutants was aligned with chlorophyll (Chl) content and chloroplast development. The map-based cloning and molecular complementation showed that TCD11 encodes the ribosomal small subunit protein S6 in chloroplasts (RPS6). TCD11 was abundantly expressed in leaves, suggesting its different expressions in tissues. In addition, the disruption of TCD11 greatly reduced the transcript levels of certain chloroplasts-associated genes and prevented the assembly of ribosome in chloroplasts at low temperature (20°C), whereas they recovered to nearly normal levels at high temperature (32°C). Thus, our data indicate that TCD11 plays an important role in chloroplast development at low temperature. Upon our knowledge, the observations from this study provide a first glimpse into the importance of RPS6 function in rice chloroplast development.
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Affiliation(s)
- Wen-Juan Wang
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kai-Lun Zheng
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiao-Di Gong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China; Institute of Genetics and Developmental Biology Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 10010, China
| | - Jian-Long Xu
- The Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan Cun Street, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ji-Rong Huang
- Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dong-Zhi Lin
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Yan-Jun Dong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
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16
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Zheng K, Zhao J, Lin D, Chen J, Xu J, Zhou H, Teng S, Dong Y. The Rice TCM5 Gene Encoding a Novel Deg Protease Protein is Essential for Chloroplast Development under High Temperatures. RICE (NEW YORK, N.Y.) 2016; 9:13. [PMID: 27000876 PMCID: PMC4801845 DOI: 10.1186/s12284-016-0086-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/08/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND High temperature affects a broad spectrum of cellular components and metabolism in plants. The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms. Deg proteases are required for the survival of Escherichia coli at high temperatures. However, it is still unclear whether rice Deg proteases are required for chloroplast development under high temperatures. RESULTS In this study, we reported the first rice deg mutant tcm5 (thermo-sensitive chlorophyll-deficient mutant 5) that has an albino phenotype, defective chloroplasts and could not survive after the 4-5 leaf seedling stage when grown at high temperature (32 °C). However, when grown at low temperatures (20 °C), tcm5 has a normal phenotype. Map-based cloning showed that TCM5 encoding a chloroplast-targeted Deg protease protein. The TCM5 transcripts were highly expressed in all green tissues and undetectable in other tissues, showing the tissue-specific expression. In tcm5 mutants grown at high temperatures, the transcript levels of certain genes associated with chloroplast development especially PSII-associated genes were severely affected, but recovered to normal levels at low temperatures. These results showed important role of TCM5 for chloroplast development under high temperatures. CONCLUSIONS The TCM5 encodes chloroplast-targeted Deg protease protein which is important for chloroplast development and the maintenance of PSII function and its disruption would lead to a defective chloroplast and affected expression levels of genes associated with chloroplast development and photosynthesis at early rice seedling stage under high temperatures.
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Affiliation(s)
- Kailun Zheng
- />Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234 China
| | - Jian Zhao
- />Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234 China
- />Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Dongzhi Lin
- />Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234 China
| | - Jiaying Chen
- />Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234 China
- />Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Jianlong Xu
- />Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan Cun Street, Beijing, 100081 China
| | - Hua Zhou
- />Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234 China
- />Present address: Agricultural Faculty, Hokkaido University, Sappro, 060-0817 Japan
| | - Sheng Teng
- />Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Yanjun Dong
- />Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234 China
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Abe K, Ichikawa H. Gene Overexpression Resources in Cereals for Functional Genomics and Discovery of Useful Genes. FRONTIERS IN PLANT SCIENCE 2016; 7:1359. [PMID: 27708649 PMCID: PMC5030214 DOI: 10.3389/fpls.2016.01359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/26/2016] [Indexed: 05/12/2023]
Abstract
Identification and elucidation of functions of plant genes is valuable for both basic and applied research. In addition to natural variation in model plants, numerous loss-of-function resources have been produced by mutagenesis with chemicals, irradiation, or insertions of transposable elements or T-DNA. However, we may be unable to observe loss-of-function phenotypes for genes with functionally redundant homologs and for those essential for growth and development. To offset such disadvantages, gain-of-function transgenic resources have been exploited. Activation-tagged lines have been generated using obligatory overexpression of endogenous genes by random insertion of an enhancer. Recent progress in DNA sequencing technology and bioinformatics has enabled the preparation of genomewide collections of full-length cDNAs (fl-cDNAs) in some model species. Using the fl-cDNA clones, a novel gain-of-function strategy, Fl-cDNA OvereXpressor gene (FOX)-hunting system, has been developed. A mutant phenotype in a FOX line can be directly attributed to the overexpressed fl-cDNA. Investigating a large population of FOX lines could reveal important genes conferring favorable phenotypes for crop breeding. Alternatively, a unique loss-of-function approach Chimeric REpressor gene Silencing Technology (CRES-T) has been developed. In CRES-T, overexpression of a chimeric repressor, composed of the coding sequence of a transcription factor (TF) and short peptide designated as the repression domain, could interfere with the action of endogenous TF in plants. Although plant TFs usually consist of gene families, CRES-T is effective, in principle, even for the TFs with functional redundancy. In this review, we focus on the current status of the gene-overexpression strategies and resources for identifying and elucidating novel functions of cereal genes. We discuss the potential of these research tools for identifying useful genes and phenotypes for application in crop breeding.
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Affiliation(s)
| | - Hiroaki Ichikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research OrganizationTsukuba, Japan
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19
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Li R, Li J, Li S, Qin G, Novák O, Pěnčík A, Ljung K, Aoyama T, Liu J, Murphy A, Gu H, Tsuge T, Qu LJ. ADP1 affects plant architecture by regulating local auxin biosynthesis. PLoS Genet 2014; 10:e1003954. [PMID: 24391508 PMCID: PMC3879159 DOI: 10.1371/journal.pgen.1003954] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/26/2013] [Indexed: 01/30/2023] Open
Abstract
Plant architecture is one of the key factors that affect plant survival and productivity. Plant body structure is established through the iterative initiation and outgrowth of lateral organs, which are derived from the shoot apical meristem and root apical meristem, after embryogenesis. Here we report that ADP1, a putative MATE (multidrug and toxic compound extrusion) transporter, plays an essential role in regulating lateral organ outgrowth, and thus in maintaining normal architecture of Arabidopsis. Elevated expression levels of ADP1 resulted in accelerated plant growth rate, and increased the numbers of axillary branches and flowers. Our molecular and genetic evidence demonstrated that the phenotypes of plants over-expressing ADP1 were caused by reduction of local auxin levels in the meristematic regions. We further discovered that this reduction was probably due to decreased levels of auxin biosynthesis in the local meristematic regions based on the measured reduction in IAA levels and the gene expression data. Simultaneous inactivation of ADP1 and its three closest homologs led to growth retardation, relative reduction of lateral organ number and slightly elevated auxin level. Our results indicated that ADP1-mediated regulation of the local auxin level in meristematic regions is an essential determinant for plant architecture maintenance by restraining the outgrowth of lateral organs. Plant architecture is one of the key factors that affect plant survival and productivity. It is well established that the plant hormone auxin plays an essential role in organ initiation and pattern formation, thus affecting plant architecture. We found that a putative MATE (multidrug and toxic compound extrusion) transporter, ADP1, which was expressed in the meristematic regions, through regulating the level of auxin biosynthesis, controls lateral organ outgrowth so as to maintain normal architecture in Arabidopsis. The more ADP1 was expressed, the less levels of local auxin were detected in the meristematic regions of the plant, resulting in increased growth rate and a greater number of axillary branches and flowers. The reduction of auxin levels is probably due to decreased level of auxin biosynthesis in the local meristematic regions. Down-regulated expression of ADP1 and its three closely related genes caused plants to grow slower and to produce less lateral organs. Our results indicated that ADP1-mediated regulation of the local auxin levels in meristematic regions is an essential determinant for plant architecture by restraining the outgrowth of lateral organs.
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Affiliation(s)
- Ruixi Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Jieru Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Shibai Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Ondřej Novák
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 21, Olomouc, Czech Republic
| | - Aleš Pěnčík
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto, Japan
| | - Jingjing Liu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Angus Murphy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, People's Republic of China
- National Plant Gene Research Center (Beijing), Beijing, People's Republic of China
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto, Japan
- * E-mail: (TT); (LJQ)
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, People's Republic of China
- National Plant Gene Research Center (Beijing), Beijing, People's Republic of China
- * E-mail: (TT); (LJQ)
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Identification and characterization of BGL11(t), a novel gene regulating leaf-color mutation in rice (Oryza sativa L.). Genes Genomics 2013. [DOI: 10.1007/s13258-013-0094-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Zhang F, Luo X, Hu B, Wan Y, Xie J. YGL138(t), encoding a putative signal recognition particle 54 kDa protein, is involved in chloroplast development of rice. RICE (NEW YORK, N.Y.) 2013; 6:7. [PMID: 24280537 PMCID: PMC4883693 DOI: 10.1186/1939-8433-6-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 03/20/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Normal development of chloroplast is vitally important to plants, but its biological mechanism is still far from fully being understood, especially in rice. RESULTS In this study, a novel yellow-green leaf mutant, ygl138, derived from Nipponbare (Oryza sativa L. ssp. japonica) treated by ethyl methanesulfonate (EMS), was isolated. The mutant exhibited a distinct yellow-green leaf phenotype throughout development, reduced chlorophyll level, and arrested chloroplast development. The phenotype of the ygl138 mutant was caused by a single nuclear gene, which was tentatively designed as YGL138(t). The YGL138(t) locus was mapped to chromosome 11 and isolated into a confined region of 91.8 kb by map-based cloning. Sequencing analysis revealed that, Os11g05552, which was predicted to encode a signal recognition particle 54 kDa (SRP54) protein and act as a chloroplast precursor, had 18 bp nucleotides deletion in the coding region of ygl138 and led to a frameshift. Furthermore, the identity of Os11g05552 was verified by transgenic complementation. CONCLUSIONS These results are very valuable for further study on YGL138(t) gene and illuminating the mechanism of SRP54 protein involving in chloroplast development of rice.
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Affiliation(s)
- Fantao Zhang
- />College of Life Sciences, Jiangxi Normal University, Nanchang, 330022 China
| | - Xiangdong Luo
- />College of Life Sciences, Jiangxi Normal University, Nanchang, 330022 China
| | - Biaolin Hu
- />Biotechnology Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Yong Wan
- />Biotechnology Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Jiankun Xie
- />College of Life Sciences, Jiangxi Normal University, Nanchang, 330022 China
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Jeng TL, Shih YJ, Ho PT, Lai CC, Lin YW, Wang CS, Sung JM. γ-Oryzanol, tocol and mineral compositions in different grain fractions of giant embryo rice mutants. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:1468-74. [PMID: 22131276 DOI: 10.1002/jsfa.4728] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 09/16/2011] [Accepted: 09/27/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rice embryo is concentrated with lipid, protein and some bioactive chemicals. Two rice mutants IR64-GE and TNG71-GE (M7 generation) were characterised by an enlarged embryo compared with their wild types. In the present study, distributions of protein, lipid, total phenolics, γ-oryzanol, tocols and some essential minerals in these two giant embryo mutants and their respective normal embryo wild types IR64 and TNG71 were compared. RESULTS The embryo dry weights of giant embryo mutants IR64-GE and TNG71-GE were 0.92 and 1.32 mg per seed respectively. These values were higher than those of their respective normal embryo genotypes (0.50 and 0.62 mg per seed). Large variations in protein, lipid, phenolic, γ-oryzanol, tocol and minerals levels were found between mutant and wild-type pairs. The brown rice of TNG71-GE had higher total γ-oryzanol (average of 24% increase) and total tocol (average of 75% increase) levels than TNG71, IR64 and IR64-GE. CONCLUSION The embryo and bran parts of giant embryo mutant TNG71-GE were found to be good sources of vitamin E and γ-oryzanol. Therefore it could be used to produce high-value by-products from milled embryo and bran parts and as a genetic resource for rice improvement programmes. TNG71-GE can also be used as a nutrient-fortified rice cultivar.
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Affiliation(s)
- Toong Long Jeng
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung County, Taiwan
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Xue LJ, Zhang JJ, Xue HW. Genome-wide analysis of the complex transcriptional networks of rice developing seeds. PLoS One 2012; 7:e31081. [PMID: 22363552 PMCID: PMC3281924 DOI: 10.1371/journal.pone.0031081] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 01/02/2012] [Indexed: 11/18/2022] Open
Abstract
Background The development of rice (Oryza sativa) seed is closely associated with assimilates storage and plant yield, and is fine controlled by complex regulatory networks. Exhaustive transcriptome analysis of developing rice embryo and endosperm will help to characterize the genes possibly involved in the regulation of seed development and provide clues of yield and quality improvement. Principal Findings Our analysis showed that genes involved in metabolism regulation, hormone response and cellular organization processes are predominantly expressed during rice development. Interestingly, 191 transcription factor (TF)-encoding genes are predominantly expressed in seed and 59 TFs are regulated during seed development, some of which are homologs of seed-specific TFs or regulators of Arabidopsis seed development. Gene co-expression network analysis showed these TFs associated with multiple cellular and metabolism pathways, indicating a complex regulation of rice seed development. Further, by employing a cold-resistant cultivar Hanfeng (HF), genome-wide analyses of seed transcriptome at normal and low temperature reveal that rice seed is sensitive to low temperature at early stage and many genes associated with seed development are down-regulated by low temperature, indicating that the delayed development of rice seed by low temperature is mainly caused by the inhibition of the development-related genes. The transcriptional response of seed and seedling to low temperature is different, and the differential expressions of genes in signaling and metabolism pathways may contribute to the chilling tolerance of HF during seed development. Conclusions These results provide informative clues and will significantly improve the understanding of rice seed development regulation and the mechanism of cold response in rice seed.
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Affiliation(s)
- Liang-Jiao Xue
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing-Jing Zhang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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Jeng TL, Ho PT, Shih YJ, Lai CC, Wu MT, Sung JM. Comparisons of protein, lipid, phenolics, γ-oryzanol, vitamin E, and mineral contents in bran layer of sodium azide-induced red rice mutants. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2011; 91:1459-65. [PMID: 21337583 DOI: 10.1002/jsfa.4333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 01/07/2011] [Accepted: 01/10/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND The bran part of red rice grain is concentrated with many phytochemicals, including proanthocyanidins, oryzanol and vitamin E, that exert beneficial effects on human health, but it contains low levels of essential minerals such as Fe and Zn. In the present study, the protein, lipid, phytochemicals and mineral contents in bran samples were compared among red rice SA-586 and its NaN₃-induced mutants. RESULTS The plant heights of NaN₃-induced mutants were decreased. The contents of protein, lipid, total phenolics, total flavonoids, total anthocyanins, total proanthocyanidins, total γ-oryzanol, total tocopherols and total tocotrienols also varied among the tested mutants. The brans of mutants M-18, M-56 and M-50 contained more proanthocyanidins, γ-oryzanol, vitamin E than that of SA-586, respectively. M-54 accumulated more Fe content (588.7 mg kg⁻¹ bran dry weight) than SA-586 (100.1 mg kg⁻¹ bran dry weight). CONCLUSIONS The brans of M-18, M-50 and M-56 are good sources of proanthocyanidins, vitamin E and γ-oryzanol, respectively, while the bran of M-54 is rich in Fe. Thus these mutants could be used to produce high-value phytochemicals or Fe byproducts from bran during rice grain milling or as genetic resources for rice improvement programs.
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Affiliation(s)
- Toong Long Jeng
- Biotechnology division, Taiwan Agricultural Research Institute, Wufeng, Taichung County, Taiwan, ROC
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25
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Sozzani R, Benfey PN. High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype. Genome Biol 2011; 12:219. [PMID: 21457493 PMCID: PMC3129668 DOI: 10.1186/gb-2011-12-3-219] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
High-throughput phenotyping approaches (phenomics) are being combined with genome-wide genetic screens to identify alterations in phenotype that result from gene inactivation. Here we highlight promising technologies for 'phenome-scale' analyses in multicellular organisms.
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Affiliation(s)
- Rosangela Sozzani
- Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, North Carolina, USA
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26
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Chern CG, Fan MJ, Huang SC, Yu SM, Wei FJ, Wu CC, Trisiriroj A, Lai MH, Chen S, Hsing YIC. Methods for rice phenomics studies. Methods Mol Biol 2011; 678:129-138. [PMID: 20931377 DOI: 10.1007/978-1-60761-682-5_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
With the completion of the rice genome sequencing project, the next major challenge is the large-scale determination of gene function. A systematic phenotypic profiling of mutant collections will provide major insights into gene functions important for crop growth or production. Thus, detailed phenomics analysis is the key to functional genomics. Currently, the two major types of rice mutant collections are insertional mutants and chemical or irradiation-induced mutants. Here we describe how to manipulate a rice mutant population, including conducting phenomics studies and the subsequent propagation and seed storage. We list the phenotypes screened and also describe how to collect data systematically for a database of the qualitative and quantitative phenotypic traits. Thus, data on mutant lines, phenotypes, and segregation rate for all kinds of mutant populations, as well as integration sites for insertional mutant populations, would be searchable, and the collection would be a good resource for rice functional genomics study.
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Affiliation(s)
- Chyr-Guan Chern
- Taiwan Agricultural Research Institute, Wufeng, Taichung, Taiwan
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27
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Jiang SY, Ramachandran S. Functional genomics of rice pollen and seed development by genome-wide transcript profiling and Ds insertion mutagenesis. Int J Biol Sci 2010; 7:28-40. [PMID: 21209789 PMCID: PMC3014553 DOI: 10.7150/ijbs.7.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 12/27/2010] [Indexed: 01/10/2023] Open
Abstract
Rice pollen and seed development are directly related to grain yield. To further improve rice yield, it is important for us to functionally annotate the genes controlling pollen/seed development and to use them for rice breeding. Here we first carried out a genome-wide expression analysis with an emphasis on genes being involved in rice pollen and seed development. Based on the transcript profiling, we have identified and functionally classified 82 highly expressed pollen-specific, 12 developing seed-specific and 19 germinating seed-specific genes. We then presented the utilization of the maize transposon Dissociation (Ds) insertion lines for functional genomics of rice pollen and seed development and as alternative germplasm resources for rice breeding. We have established a two-element Activator/Dissociation (Ac/Ds) gene trap tagging system and generated around 20,000 Ds insertion lines. We have subjected these lines for screens to obtain high and low yield Ds insertion lines. Some interesting lines have been obtained with higher yield or male sterility. Flanking Sequence Tags (FSTs) analyses showed that these Ds-tagged genes encoded various proteins including transcription factors, transport proteins, unknown functional proteins and so on. They exhibited diversified expression patterns. Our results suggested that rice could be improved not only by introducing foreign genes but also by knocking out its endogenous genes. This finding might provide a new way for rice breeder to further improve rice varieties.
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Affiliation(s)
- Shu-Ye Jiang
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604
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28
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Physiological character and molecular mapping of leaf-color mutant wyv1 in rice (Oryza sativa L.). Genes Genomics 2010. [DOI: 10.1007/s13258-009-0794-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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29
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Sano CM, Bohn MO, Paige KN, Jacobs TW. Heritable variation in the inflorescence replacement program of Arabidopsis thaliana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1461-1476. [PMID: 19787332 DOI: 10.1007/s00122-009-1148-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 08/30/2009] [Indexed: 05/28/2023]
Abstract
Owing to their sessile habits and trophic position within global ecosystems, higher plants display a sundry assortment of adaptations to the threat of predation. Unlike animals, nearly all higher plants can replace reproductive structures lost to predators by activating reserved growing points called axillary meristems. As the first step in a program aimed at defining the genetic architecture of the inflorescence replacement program (IRP) of Arabidopsis thaliana, we describe the results of a quantitative germplasm survey of developmental responses to loss of the primary reproductive axis. Eighty-five diverse accessions were grown in a replicated common garden and assessed for six life history traits and four IRP traits, including the number and lengths of axillary inflorescences present on the day that the first among them re-flowered after basal clipping of the primary inflorescence. Significant natural variation and high heritabilities were observed for all measured characters. Pairwise correlations among the 10 focal traits revealed a multi-dimensional phenotypic space sculpted by ontogenic and plastic allometries as well as apparent constraints and outliers of genetic interest. Cluster analysis of the IRP traits sorted the 85 accessions into 5 associations, a topology that establishes the boundaries within which the evolving Arabidopsis genome extends and restricts the species' IRP repertoire to that observable worldwide.
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Affiliation(s)
- Cecile M Sano
- Department of Plant Biology, University of Illinois, 191 Edward R. Madigan Laboratory, 1201 West Gregory Drive, Urbana, IL, 61801, USA
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30
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Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M. Phenome analysis in plant species using loss-of-function and gain-of-function mutants. PLANT & CELL PHYSIOLOGY 2009; 50:1215-31. [PMID: 19502383 PMCID: PMC2709550 DOI: 10.1093/pcp/pcp078] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 05/29/2009] [Indexed: 05/20/2023]
Abstract
Analysis of genetic mutations is one of the most effective ways to investigate gene function. We now have methods that allow for mass production of mutant lines and cells in a variety of model species. Recently, large numbers of mutant lines have been generated by both 'loss-of-function' and 'gain-of-function' techniques. In parallel, phenotypic information covering various mutant resources has been acquired and released in web-based databases. As a result, significant progress in comprehensive phenotype analysis is being made through the use of these tools. Arabidopsis and rice are two major model plant species in which genome sequencing projects have been completed. Arabidopsis is the most widely used experimental plant, with a large number of mutant resources and several examples of systematic phenotype analysis. Rice is a major crop species and is used as a model plant, with an increasing number of mutant resources. Other plant species are also being employed in functional genetics research. In this review, the present status of mutant resources for large-scale studies of gene function in plant research and the current perspective on using loss-of-function and gain-of-function mutants in phenome research will be discussed.
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Affiliation(s)
- Takashi Kuromori
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Shinya Takahashi
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510 Japan
| | - Youichi Kondou
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Minami Matsui
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
- *Corresponding author: E-mail, ; Fax, +81-45-503-9584
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31
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Dong HX, Li HX, Xie GS, Zeng HL. Identification of Differentially Expressed Proteins Associated with Chlorophyll-Deficient Mutant Rice. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/ajps.2009.344.352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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32
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Wang WY, Ding HF, Li GX, Jiang MS, Li RF, Liu X, Zhang Y, Yao FY. Delimitation of the PSH1(t) gene for rice purple leaf sheath to a 23.5 kb DNA fragment. Genome 2009; 52:268-74. [PMID: 19234555 DOI: 10.1139/g08-121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Leaf sheath color plays an important role as a marker for rice genetic improvement. A recombinant inbred line (RIL) population consisting of 220 individuals was developed from a cross between an Oryza sativa subsp. indica variety, IRBB60, and an Oryza sativa subsp. japonica variety, 9407. Within the RIL population, a line, RI51, was found to have purple leaf sheath (PSH). To map the gene governing PSH, RI51 was crossed with 9407 green leaf sheath (GSH) to develop an F2 segregating population. The distribution of F2 plants with PSH and GSH fitted a segregation ratio of 3:1, indicating that the PSH was controlled by a major dominant gene. The gene locus for PSH, tentatively designated as PSH1(t), was identified by surveying two bulks made of the respective 40 individuals with PSH and GSH with SSR markers covering the entire rice genome. The survey indicated that the PSH1(t) region was located on chromosome 1. Further confirmation was made using a large random sample of 360 individuals from the same F2 population and the PSH1(t) locus was then mapped on chromosome 1 between SSR markers RM3475 and RM7202 with genetic distances of 2.0 and 1.1 cM, respectively. For fine mapping of PSH1(t), a large F(2:3) segregating population with 3300 individuals from the seven heterozygous F2 plants in the RM3475-RM7202 region was constructed. Analysis of recombinants in the PSH1(t) region anchored the gene locus to an interval of 23.5 kb flanked by the left marker L03 and the right marker L05. Sequence analysis of this fragment predicted six open reading frames encoding a putative trans-sialidase, a putative Plastidic ATP/ADP-transporter, and four unknown proteins. The detailed genetic and physical maps of the PSH1(t) locus will be very useful in molecular cloning of the PSH1(t) gene.
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Affiliation(s)
- Wen-Ying Wang
- High-Tech Research Center, Shandong Academy of Agricultural Science, Jinan 250100, P.R. China
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33
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Gene mapping related to yellow green leaf in a mutant line in rice (Oryza sativa L.). Genes Genomics 2009. [DOI: 10.1007/bf03191149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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34
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Sabelli PA, Larkins BA. The development of endosperm in grasses. PLANT PHYSIOLOGY 2009; 149:14-26. [PMID: 19126691 PMCID: PMC2613697 DOI: 10.1104/pp.108.129437] [Citation(s) in RCA: 264] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 10/18/2008] [Indexed: 05/18/2023]
Affiliation(s)
- Paolo A Sabelli
- Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
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35
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Xiao X, Yang Y, Yang Y, Lin J, Tang D, Liu X. Comparative analysis of young panicle proteome in thermo-sensitive genic male-sterile rice Zhu-1S under sterile and fertile conditions. Biotechnol Lett 2008; 31:157-61. [PMID: 18923912 DOI: 10.1007/s10529-008-9838-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 08/18/2008] [Accepted: 08/19/2008] [Indexed: 11/30/2022]
Abstract
Proteome analysis was carried out to identify the young panicle proteins during different developmental stages under sterile and fertile conditions. Based on spot quantity and quality, 50 protein spots were analyzed by matrix associated laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and 20 spots were identified. Most of these proteins are closely associated with energy metabolism, protein biosynthesis, cell wall formation and stress responses, which are essential cell activities to the pollen development. Gene expression analysis of three different proteins by semi-quantitative RT-PCR showed that the mRNA level was not correlated exactly with the protein level.
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Affiliation(s)
- Xiaojuan Xiao
- College of Life Science and Biotechnology, Hunan University, Changsha, China
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36
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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.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 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] [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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Lee J, Park JJ, Kim SL, Yim J, An G. Mutations in the rice liguleless gene result in a complete loss of the auricle, ligule, and laminar joint. PLANT MOLECULAR BIOLOGY 2007; 65:487-99. [PMID: 17594063 DOI: 10.1007/s11103-007-9196-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Accepted: 05/24/2007] [Indexed: 05/08/2023]
Abstract
The area between the upper part of the leaf sheath and the basal portion of the leaf blade contains several specialized organs, such as the laminar joint, auricle and ligule. Here we report the identification of T-DNA insertional mutant lines that lack all of these organs. The gene knocked out in the mutant lines encodes a protein that contains a SBP (SQUAMOSA promoter Binding Protein)-domain and is highly homologous to the maize LIGULELESS1 (LG1) gene. At the amino acid sequence level, the OsLG1 protein is 69% identical to maize LG1 and 78% identical to barley LG1. We named the rice gene OsLIGULELESS1 (OsLG1). Transient expression of an OsLG1:RFP (Red Fluorescent Protein) fusion protein indicated that the protein is localized to the nucleus. Transgenic plants harboring the OsLG1 promoter:GUS (beta-glucuronidase) reporter gene construct display preferential expression in developing laminar joint regions and meristemic regions. The gene is also weakly expressed in the ligule, auricles, and leaf sheaths at the basal region. These results indicate that OsLG1 is a transcriptional factor that plays an important role in building the laminar joint between leaf blade and leaf sheath boundary, thereby controlling ligule and auricle development.
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Affiliation(s)
- Jinwon Lee
- National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Hyo-ja dong, Pohang, Kyungbuk 790-784, Korea
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Suzuki T, Eiguchi M, Kumamaru T, Satoh H, Matsusaka H, Moriguchi K, Nagato Y, Kurata N. MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol Genet Genomics 2007; 279:213-23. [PMID: 17952471 DOI: 10.1007/s00438-007-0293-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 09/12/2007] [Accepted: 09/17/2007] [Indexed: 02/07/2023]
Abstract
Mutant populations are indispensable genetic resources for functional genomics in all organisms. However, suitable rice mutant populations, induced either by chemicals or irradiation still have been rarely developed to date. To produce mutant pools and to launch a search system for rice gene mutations, we developed mutant populations of Oryza sativa japonica cv. Taichung 65, by treating single zygotic cells with N-methyl-N-nitrosourea (MNU). Mutagenesis in single zygotes can create mutations at a high frequency and rarely forms chimeric plants. A modified TILLING system using non-labeled primers and fast capillary gel electrophoresis was applied for high-throughput detection of single nucleotide substitution mutations. The mutation rate of an M(2) mutant population was calculated as 7.4 x 10(-6) per nucleotide representing one mutation in every 135 kb genome sequence. One can expect 7.4 single nucleotide substitution mutations in every 1 kb of gene region when using 1,000 M(2) mutant lines. The mutations were very evenly distributed over the regions examined. These results indicate that our rice mutant population generated by MNU-mutagenesis could be a promising resource for identifying mutations in any gene of rice. The modified TILLING method also proved very efficient and convenient in screening the mutant population.
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Affiliation(s)
- Tadzunu Suzuki
- Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
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39
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Liu X, Wang S, Wang Y, Wei S. Genetic analysis and molecular mapping of a nuclear recessive male sterility gene, ms91(t), in rice. Genome 2007; 50:796-801. [PMID: 17893719 DOI: 10.1139/g07-060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mutations that result in plant male sterility provide means not only to probe reproductive development but also to facilitate commercial heterosis application and hybrid seed production. In this study, we report a novel male sterility gene, ms91(t), in a spontaneous mutant line (SH38) from a Chinese rice cultivar (Oryza sativa subsp. japonica ‘Jijing14’). The sterility of SH38 was studied by examining its progenies derived from crosses with 6 japonica cultivars. Corresponding F2 populations were obtained by selfing each of the 6 F1s and a backcross population was produced by crossing SH38 to the F1 of SH38 × C18. Our results revealed that SH38 has normal agronomic traits but produces no pollen grains. Segregations of male-sterile and male-fertile progenies in the F2 and backcross populations fit well with ratios of 3:1 and 1:1, respectively, indicating that ms91(t) is a single recessive gene. Amplified fragment length polymorphism (AFLP) analysis of SH38 and Jijing14 plants showed the presence of a unique band in SH38. Simple sequence repeat (SSR) analysis of the bulked and individual progenies of the F2 population of SH38 × C18 showed linkage of ms91(t) with the SSR marker RM5853 on chromosome 1. Subsequently, ms91(t) was fine-mapped to the interval between markers RM7075 (3.75 cM) and RM5638 (3.57 cM). Our results would facilitate the isolation of ms91(t) and male sterility in heterosis application.
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Affiliation(s)
- Xia Liu
- Biology Department, Nankai University, Tianjin, China
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40
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Liu W, Fu Y, Hu G, Si H, Zhu L, Wu C, Sun Z. Identification and fine mapping of a thermo-sensitive chlorophyll deficient mutant in rice (Oryza sativa L.). PLANTA 2007; 226:785-95. [PMID: 17541632 DOI: 10.1007/s00425-007-0525-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Accepted: 04/10/2007] [Indexed: 05/06/2023]
Abstract
A thermo-sensitive chlorophyll deficient mutant was isolated from more than 15,000 transgenic rice lines. The mutant displayed normal phenotype at 23 degrees C or lower temperature (permissive temperature). However, when grown at 26 degrees C or higher (nonpermissive temperature) the plant exhibited an abnormal phenotype characterized by yellow green leaves. Genetic analysis revealed that a single nuclear-encoded recessive gene is responsible for the mutation, which is tentatively designed as cde1(t) (chlorophyll deficient 1, temporally). PCR analysis and hygromycin resistance assay indicated the mutation was not caused by T-DNA insertion. To isolate the cde1(t) gene, a map-based cloning strategy was employed and 15 new markers (five SSR and ten InDels markers) were developed. A high-resolution physical map of the chromosomal region around the cde1(t) gene was made using F(2) and F(3) population consisting of 1,858 mutant individuals. Finally, the cde1(t) gene was mapped in 7.5 kb region between marker ID10 and marker ID11 on chromosome 2. Sequence analysis revealed only one candidate gene, OsGluRS, in the 7.5 kb region. Cloning and sequencing of the target region from the cde1(t) mutant showed that a missense mutation occurred in the mutant. So the OsGluRS gene (TIGR locus Os02 g02860) which encode glutamyl-tRNA synthetase was identified as the Cde1(t) gene.
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Affiliation(s)
- Wenzhen Liu
- College of Life Sciences, Zhejiang University, 310029 Hangzhou, ZJ, China
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41
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Vij S, Tyagi AK. Emerging trends in the functional genomics of the abiotic stress response in crop plants. PLANT BIOTECHNOLOGY JOURNAL 2007; 5:361-80. [PMID: 17430544 DOI: 10.1111/j.1467-7652.2007.00239.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plants are exposed to different abiotic stresses, such as water deficit, high temperature, salinity, cold, heavy metals and mechanical wounding, under field conditions. It is estimated that such stress conditions can potentially reduce the yield of crop plants by more than 50%. Investigations of the physiological, biochemical and molecular aspects of stress tolerance have been conducted to unravel the intrinsic mechanisms developed during evolution to mitigate against stress by plants. Before the advent of the genomics era, researchers primarily used a gene-by-gene approach to decipher the function of the genes involved in the abiotic stress response. However, abiotic stress tolerance is a complex trait and, although large numbers of genes have been identified to be involved in the abiotic stress response, there remain large gaps in our understanding of the trait. The availability of the genome sequences of certain important plant species has enabled the use of strategies, such as genome-wide expression profiling, to identify the genes associated with the stress response, followed by the verification of gene function by the analysis of mutants and transgenics. Certain components of both abscisic acid-dependent and -independent cascades involved in the stress response have already been identified. Information originating from the genome-wide analysis of abiotic stress tolerance will help to provide an insight into the stress-responsive network(s), and may allow the modification of this network to reduce the loss caused by stress and to increase agricultural productivity.
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Affiliation(s)
- Shubha Vij
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Chen R, Zhao X, Shao Z, Wei Z, Wang Y, Zhu L, Zhao J, Sun M, He R, He G. Rice UDP-glucose pyrophosphorylase1 is essential for pollen callose deposition and its cosuppression results in a new type of thermosensitive genic male sterility. THE PLANT CELL 2007; 19:847-61. [PMID: 17400897 PMCID: PMC1867369 DOI: 10.1105/tpc.106.044123] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
UDP-glucose pyrophosphorylase (UGPase) catalyzes the reversible production of glucose-1-phosphate and UTP to UDP-glucose and pyrophosphate. The rice (Oryza sativa) genome contains two homologous UGPase genes, Ugp1 and Ugp2. We report a functional characterization of rice Ugp1, which is expressed throughout the plant, with highest expression in florets, especially in pollen during anther development. Ugp1 silencing by RNA interference or cosuppression results in male sterility. Expressing a double-stranded RNA interference construct in Ugp1-RI plants resulted in complete suppression of both Ugp1 and Ugp2, together with various pleiotropic developmental abnormalities, suggesting that UGPase plays critical roles in plant growth and development. More importantly, Ugp1-cosuppressing plants contained unprocessed intron-containing primary transcripts derived from transcription of the overexpression construct. These aberrant transcripts undergo temperature-sensitive splicing in florets, leading to a novel thermosensitive genic male sterility. Pollen mother cells (PMCs) of Ugp1-silenced plants appeared normal before meiosis, but during meiosis, normal callose deposition was disrupted. Consequently, the PMCs began to degenerate at the early meiosis stage, eventually resulting in complete pollen collapse. In addition, the degeneration of the tapetum and middle layer was inhibited. These results demonstrate that rice Ugp1 is required for callose deposition during PMC meiosis and bridges the apoplastic unloading pathway and pollen development.
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Affiliation(s)
- Rongzhi Chen
- Key Laboratory of Ministry of Education for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Miyabayashi T, Nonomura KI, Morishima H, Kurata N. Genome Size of Twenty Wild Species of Oryza Determined by Flow Cytometric and Chromosome Analyses. BREEDING SCIENCE 2007; 57:73-78. [PMID: 0 DOI: 10.1270/jsbbs.57.73] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
| | - Ken-Ichi Nonomura
- National Institute of Genetics
- Graduate University for Advanced Studies/Sokendai
| | | | - Nori Kurata
- National Institute of Genetics
- Graduate University for Advanced Studies/Sokendai
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Yang Q, Liang C, Zhuang W, Li J, Deng H, Deng Q, Wang B. Characterization and identification of the candidate gene of rice thermo-sensitive genic male sterile gene tms5 by mapping. PLANTA 2007; 225:321-30. [PMID: 16896793 DOI: 10.1007/s00425-006-0353-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Accepted: 06/22/2006] [Indexed: 05/07/2023]
Abstract
Previous research has demonstrated that the thermo-sensitive genic male-sterile (TGMS) gene in rice was regulated by temperature. TGMS rice is important to hybrid rice production because the application of the TGMS system in two-line breeding is cost-effective, simple, efficient and overcomes the limitations of the cytoplasmic male sterility (CMS) system. AnnongS is the first discovered and deeply studied TGMS rice line in China. Previous studies have suggested that AnnongS-1 and Y58S, two derivative TGMS lines of AnnongS, were both controlled by a single recessive gene named tms5, which was genetically mapped on chromosome 2. In the current study, three populations (AnnongS-1 x Nanjing11, Y58S x Q611, and Y58S x Guanghui122) were developed to investigate the tms5 gene molecular map. Analysis of recombination events of sterile samples, utilizing 125 probes covering the tms5 region, suggested that the tms5 gene was physically mapped to a 19 kb DNA fragment between two markers, 4039-1 and 4039-2, located on the BAC clone AP004039. Following the construction of a physical map between the two markers, ONAC023, a member of the NAC (NAM-ATAF-CUC-related) gene family, was identified as the candidate of the tms5 gene.
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Affiliation(s)
- Qingkai Yang
- The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Molecular and biochemical analysis of the gelatinization temperature characteristics of rice (Oryza sativa L.) Starch granules. J Cereal Sci 2006. [DOI: 10.1016/j.jcs.2006.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhang K, Qian Q, Huang Z, Wang Y, Li M, Hong L, Zeng D, Gu M, Chu C, Cheng Z. GOLD HULL AND INTERNODE2 encodes a primarily multifunctional cinnamyl-alcohol dehydrogenase in rice. PLANT PHYSIOLOGY 2006; 140:972-83. [PMID: 16443696 PMCID: PMC1400561 DOI: 10.1104/pp.105.073007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Lignin content and composition are two important agronomic traits for the utilization of agricultural residues. Rice (Oryza sativa) gold hull and internode phenotype is a classical morphological marker trait that has long been applied to breeding and genetics study. In this study, we have cloned the GOLD HULL AND INTERNODE2 (GH2) gene in rice using a map-based cloning approach. The result shows that the gh2 mutant is a lignin-deficient mutant, and GH2 encodes a cinnamyl-alcohol dehydrogenase (CAD). Consistent with this finding, extracts from roots, internodes, hulls, and panicles of the gh2 plants exhibited drastically reduced CAD activity and undetectable sinapyl alcohol dehydrogenase activity. When expressed in Escherichia coli, purified recombinant GH2 was found to exhibit strong catalytic ability toward coniferaldehyde and sinapaldehyde, while the mutant protein gh2 completely lost the corresponding CAD and sinapyl alcohol dehydrogenase activities. Further phenotypic analysis of the gh2 mutant plants revealed that the p-hydroxyphenyl, guaiacyl, and sinapyl monomers were reduced in almost the same ratio compared to the wild type. Our results suggest GH2 acts as a primarily multifunctional CAD to synthesize coniferyl and sinapyl alcohol precursors in rice lignin biosynthesis.
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Affiliation(s)
- Kewei Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, People's Republic of China
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Jeong DH, An S, Park S, Kang HG, Park GG, Kim SR, Sim J, Kim YO, Kim MK, Kim SR, Kim J, Shin M, Jung M, An G. Generation of a flanking sequence-tag database for activation-tagging lines in japonica rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 45:123-32. [PMID: 16367959 DOI: 10.1111/j.1365-313x.2005.02610.x] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We have generated 47,932 T-DNA tag lines in japonica rice using activation-tagging vectors that contain tetramerized 35S enhancer sequences. To facilitate use of those lines, we isolated the genomic sequences flanking the inserted T-DNA via inverse polymerase chain reaction. For most of the lines, we performed four sets of amplifications using two different restriction enzymes toward both directions. In analyzing 41,234 lines, we obtained 27,621 flanking sequence tags (FSTs), among which 12,505 were integrated into genic regions and 15,116 into intergenic regions. Mapping of the FSTs on chromosomes revealed that T-DNA integration frequency was generally proportional to chromosome size. However, T-DNA insertions were non-uniformly distributed on each chromosome: higher at the distal ends and lower in regions close to the centromeres. In addition, several regions showed extreme peaks and valleys of insertion frequency, suggesting hot and cold spots for T-DNA integration. The density of insertion events was somewhat correlated with expressed, rather than predicted, gene density along each chromosome. Analyses of expression patterns near the inserted enhancer showed that at least half the test lines displayed greater expression of the tagged genes. Whereas in most of the increased lines expression patterns after activation were similar to those in the wild type, thereby maintaining the endogenous patterns, the remaining lines showed changes in expression in the activation tagged lines. In this case, ectopic expression was most frequently observed in mature leaves. Currently, the database can be searched with the gene locus number or location on the chromosome at http://www.postech.ac.kr/life/pfg/risd. On request, seeds of the T(1) or T(2) plants will be provided to the scientific community.
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Affiliation(s)
- Dong-Hoon Jeong
- Department of Life Science and National Research Laboratory of Plant Functional Genomics, Pohang University of Science and Technology, POSTECH, Republic of Korea
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Kurata N, Yamazaki Y. Oryzabase. An integrated biological and genome information database for rice. PLANT PHYSIOLOGY 2006; 140:12-7. [PMID: 16403737 PMCID: PMC1326027 DOI: 10.1104/pp.105.063008] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). The database contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. The anatomical description of rice development is unique and is the first known representation for rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. The systematic presentation of a large number of rice mutant and mutant trait genes is indispensable, as is description of research in wild strains, core collections, and their detailed characterization. Several genetic, physical, and expression maps with full genome and cDNA sequences are also combined with biological data in Oryzabase. These datasets, when pooled together, could provide a useful tool for gaining greater knowledge about the life cycle of rice, the relationship between phenotype and gene function, and rice genetic diversity. For exchanging community information, Oryzabase publishes the Rice Genetics Newsletter organized by the Rice Genetics Cooperative and provides a mailing service, rice-e-net/rice-net.
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Affiliation(s)
- Nori Kurata
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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Lee DS, Chen LJ, Suh HS. Genetic characterization and fine mapping of a novel thermo-sensitive genic male-sterile gene tms6 in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1271-7. [PMID: 16133314 DOI: 10.1007/s00122-005-0044-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Accepted: 07/02/2005] [Indexed: 05/04/2023]
Abstract
The application of genetic male sterility in hybrid rice production has great potential to revolutionize hybrid seed production methodology. The two-line breeding system by using thermo-sensitive genic male sterility (TGMS) has been discovered and successfully developed as a breeding strategy in rice. One TGMS gene was investigated by a spontaneous rice mutant line, Sokcho-MS, originated from a Korean japonica variety. It was shown that Sokcho-MS is completely sterile at a temperature higher than 27 degrees C and/or lower than 25 degrees C during the development of spikelets, but fertile at the temperature ranging from 25 to 27 degrees C regardless of the levels of day-length. Genetic analysis and molecular mapping based on SSR, STS and EST markers revealed that a single recessive gene locus involved the control of genic male sterility in Sokcho-MS. By using an F2 mapping population derived from a cross between Sokcho-MS and a fertile indica variety Neda, the new TGMS gene, designated as tms6, was mapped primarily to the long arm of chromosome 5 of Oryza sativa at the interval between markers E60663 (2.0 cM) and RM440 (5.8 cM). Subsequently, tms6 was fine mapped to the interval between markers RM3351 (0.1 cM) and E60663 (1.9 cM). As tms6 appeared to be independent of other mapped TGMS genes in rice, the genetic basis of Sokcho-MS was further discussed.
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Affiliation(s)
- Dong Sun Lee
- Institute of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 712-749 Korea
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Yamazaki Y, Jaiswal P. Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. PLANT & CELL PHYSIOLOGY 2005; 46:63-68. [PMID: 15659431 DOI: 10.1093/pcp/pci505] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An enormous amount of information and materials in the field of biology has been accumulating, such as nucleotide and amino acid sequences, gene and protein functions, mutants and their phenotypes, and literature references, produced by the rapid development in this field. Effective use of the information may strongly promote biological studies, and may lead to many important findings. It is, however, time-consuming and laborious for individual researchers to collect information from individual original sites and to rearrange it for their own purpose. A concept, ontology, has been introduced in biology to support and encourage researchers to share and reuse information among biological databases. Ontology has a glossary, named dynamic controlled vocabulary, in which relationships between terms are defined. Since each term is strictly defined and identified with an ID number, a set of data represented in biological ontology is easily accessible to automated information processing, even if the data sets are across several databases and/or different organisms. In this mini-review, we introduce activities in Gramene and Oryzabase, which provide biological ontologies for Oryza sativa (rice).
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Affiliation(s)
- Yukiko Yamazaki
- Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan.
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