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Xu T, Fu D, Xiong X, Zhu J, Feng Z, Liu X, Wu C. OsbHLH067, OsbHLH068, and OsbHLH069 redundantly regulate inflorescence axillary meristem formation in rice. PLoS Genet 2023; 19:e1010698. [PMID: 37053298 PMCID: PMC10128955 DOI: 10.1371/journal.pgen.1010698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 04/25/2023] [Accepted: 03/08/2023] [Indexed: 04/15/2023] Open
Abstract
Rice axillary meristems (AMs) are essential to the formation of tillers and panicle branches in rice, and therefore play a determining role in rice yield. However, the regulation of inflorescence AM development in rice remains elusive. In this study, we identified no spikelet 1-Dominant (nsp1-D), a sparse spikelet mutant, with obvious reduction of panicle branches and spikelets. Inflorescence AM deficiency in nsp1-D could be ascribed to the overexpression of OsbHLH069. OsbHLH069 functions redundantly with OsbHLH067 and OsbHLH068 in panicle AM formation. The Osbhlh067 Osbhlh068 Osbhlh069 triple mutant had smaller panicles and fewer branches and spikelets. OsbHLH067, OsbHLH068, and OsbHLH069 were preferentially expressed in the developing inflorescence AMs and their proteins could physically interact with LAX1. Both nsp1-D and lax1 showed sparse panicles. Transcriptomic data indicated that OsbHLH067/068/069 may be involved in the metabolic pathway during panicle AM formation. Quantitative RT-PCR results demonstrated that the expression of genes involved in meristem development and starch/sucrose metabolism was down-regulated in the triple mutant. Collectively, our study demonstrates that OsbHLH067, OsbHLH068, and OsbHLH069 have redundant functions in regulating the formation of inflorescence AMs during panicle development in rice.
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Affiliation(s)
- Tingting Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaohu Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Junkai Zhu
- Jiangsu Kingearth Seed Co., Ltd., Yangzhou, China
| | - Zhiyun Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaobin Liu
- Jiangsu Kingearth Seed Co., Ltd., Yangzhou, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Li S, Wang C, You C, Zhou X, Zhou H. T-LOC: A comprehensive tool to localize and characterize T-DNA integration sites. PLANT PHYSIOLOGY 2022; 190:1628-1639. [PMID: 35640125 PMCID: PMC9614469 DOI: 10.1093/plphys/kiac225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/23/2022] [Indexed: 05/30/2023]
Abstract
Scientists have developed many approaches based on PCR or next-generation sequencing to localize and characterize integrated T-DNAs in transgenic plants generated by Agrobacterium tumefaciens-mediated T-DNA transfer. However, none of these methods has the robust ability to handle all transgenic plants with diversified T-DNA patterns. Utilizing the valuable information in the whole-genome sequencing data of transgenic plants, we have developed a comprehensive approach (T-LOC) to localize and characterize T-DNA integration sites (TISs). We evaluated the performance of T-LOC on genome sequencing data from 48 transgenic rice (Oryza sativa) plants that provide real and unbiased resources of T-DNA integration patterns. T-LOC discovered 75 full TISs and reported a diversified pattern of T-DNA integration: the ideal single-copy T-DNA between two borders, multiple-copy of T-DNAs in tandem or inverted repeats, truncated partial T-DNAs with or without the selection hygromycin gene, the inclusion of T-DNA backbone, the integration at the genome repeat region, and the concatenation of multiple ideal or partial T-DNAs. In addition, we reported that DNA fragments from the two A. tumefaciens plasmids can be fused with T-DNA and integrated into the plant genome. Besides, T-LOC characterizes the genomic changes at TISs, including deletion, duplication, accurate repair, and chromosomal rearrangement. Moreover, we validated the robustness of T-LOC using PCR, Sanger sequencing, and Nanopore sequencing. In summary, T-LOC is a robust approach to studying the TISs independent of the integration pattern and can recover all types of TISs in transgenic plants.
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Affiliation(s)
| | | | - Chenjiang You
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai 200438, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Shin NR, Shin YH, Kim HS, Park YD. Function Analysis of the PR55/ B Gene Related to Self-Incompatibility in Chinese Cabbage Using CRISPR/Cas9. Int J Mol Sci 2022; 23:ijms23095062. [PMID: 35563453 PMCID: PMC9102814 DOI: 10.3390/ijms23095062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Chinese cabbage, a major crop in Korea, shows self-incompatibility (SI). SI is controlled by the type 2A serine/threonine protein phosphatases (PP2As). The PP2A gene is controlled by regulatory subunits that comprise a 36 kDa catalyst C subunit, a 65 kDa regulatory A subunit, and a variety of regulatory B subunits (50–70 kDa). Among them, the PP2A 55 kDa B regulatory subunit (PR55/B) gene located in the A05 chromosome has 13 exons spanning 2.9 kb, and two homologous genes, Bra018924 and Bra014296, were found to be present on the A06 and A08 chromosome, respectively. In this study, we performed a functional analysis of the PR55/B gene using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9)-mediated gene mutagenesis. CRISPR/Cas9 technology can be used to easily introduce mutations in the target gene. Tentative gene-edited lines were generated by the Agrobacterium-mediated transfer and were selected by PCR and Southern hybridization analysis. Furthermore, pods were confirmed to be formed in flower pollination (FP) as well as bud pollination (BP) in some gene-edited lines. Seed fertility of gene-edited lines indicated that the PR55/B gene plays a key role in SI. Finally, self-compatible T-DNA-free T2 gene-edited plants and edited sequences of target genes were secured. The self-compatible Chinese cabbage developed in this study is expected to contribute to Chinese cabbage breeding.
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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Li J, Zhang Z, Chong K, Xu Y. Chilling tolerance in rice: Past and present. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153576. [PMID: 34875419 DOI: 10.1016/j.jplph.2021.153576] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.
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Affiliation(s)
- Junhua Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Zeyong Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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Fan H, Huang LY, Tong X, Yang LJ, Shi JJ, Jiao J, Xu HQ, Li YC, Wang DY. A competitive PCR-based method to detect a single copy of T-DNA insertion in transformants. PHYSIOLOGIA PLANTARUM 2021; 173:1179-1188. [PMID: 34310717 DOI: 10.1111/ppl.13513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/05/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Gene function studies benefit from the availability of mutants. In plants, Agrobacterium-mediated genetic transformation is widely used to create mutants. These mutants, also called transformants, contain one or several transfer-DNA (T-DNA) copies in the host genome. Quantifying the copy number of T-DNA in transformants is beneficial to assess the number of mutated genes. Here, we developed a competitive polymerase chain reaction (PCR)-based method to detect a single copy of a T-DNA insertion in transformants. The competitor line BHK- -1 that contains a single copy of competitor BHK- (BHK, Basta, Hygromycin, Kanamycin-resistant genes) was crossed with test transformants and the genomic DNA of F1 plants was subjected to competitive PCR. By analyzing the gray ratio between two PCR products, we were able to determine whether or not the test transformants contained a single copy of T-DNA insertion. We also generated the control lines BHK±1:1 and BHK±2:1 , which contain the target (BHK+ ) and competitor (BHK- ) in a ratio of 1:1 and 2:1, respectively. The ratios of their PCR products are useful references for quantitative analysis. Overall, this method is reliable and simple in experimental manipulations and can be used as a substitute for Southern-blot analysis to identify a single copy of T-DNA insertion in transformants.
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Affiliation(s)
| | - Liu-Yuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Xin Tong
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Liu-Jie Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Jiao-Jiao Shi
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Jiao Jiao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Hua-Quan Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Ying-Chao Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Dan-Yang Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
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Gong W, Zhou Y, Wang R, Wei X, Zhang L, Dai Y, Zhu Z. Analysis of T-DNA integration events in transgenic rice. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153527. [PMID: 34563791 DOI: 10.1016/j.jplph.2021.153527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Agrobacterium-mediated plant transformation has been widely used for introducing transgene(s) into a plant genome and plant breeding. However, our understanding of T-DNA integration into rice genome remains limited relative to that in the model dicot Arabidopsis. To better elucidate the T-DNA integration into the rice genome, we investigated extensively the T-DNA ends and their flanking rice genomic sequences from two transgenic rice plants carrying Cowpea Trypsin Inhibitor (CpTI)-derived gene Signal-CpTI-KDEL (SCK) and Bacillus thuringiensis (BT) gene, respectively, by TAIL-PCR method. Analysis of the junction sequences between the T-DNA ends and rice genome DNA indicated that there were three joining patterns of microhomology, filler DNA sequences, and exact joining, and both the T-DNA ends tend to adopt identical manner to join the rice genome. After T-DNA integration, there were several variations of rice genomic sequences, including small deletions at the integration sites, superfluous DNA inserted between T-DNA and genome, and translocation of genomic DNA in the flanking regions. The translocation block could be from a noncontiguous region in the same chromosome or different chromosomes at the integration sites, and the originating position of the translocated block resulted in comparable deletion based on a cut/paste mechanism rather than a replication mechanism. Our study may lead to a better understand of T-DNA integration mechanism and facilitate functional genomic studies and further crop improvement.
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Affiliation(s)
- Wankui Gong
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
| | - Yun Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Rui Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Guo HM, Li HC, Zhou SR, Xue HW, Miao XX. Deficiency of mitochondrial outer membrane protein 64 confers rice resistance to both piercing-sucking and chewing insects in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1967-1982. [PMID: 32542992 DOI: 10.1111/jipb.12983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
The brown planthopper (BPH) and striped stem borer (SSB) are the most devastating insect pests in rice (Oryza sativa) producing areas. Screening for endogenous resistant genes is the most practical strategy for rice insect-resistance breeding. Forty-five mutants showing high resistance against BPH were identified in a rice T-DNA insertion population (11,000 putative homozygous lines) after 4 years of large-scale field BPH-resistance phenotype screening. Detailed analysis showed that deficiency of rice mitochondrial outer membrane protein 64 (OM64) gene resulted in increased resistance to BPH. Mitochondrial outer membrane protein 64 protein is located in the outer mitochondrial membrane by subcellular localization and its deficiency constitutively activated hydrogen peroxide (H2 O2 ) signaling, which stimulated antibiosis and tolerance to BPH. The om64 mutant also showed enhanced resistance to SSB, a chewing insect, which was due to promotion of Jasmonic acid biosynthesis and related responses. Importantly, om64 plants presented no significant changes in rice yield-related characters. This study confirmed OM64 as a negative regulator of rice herbivore resistance through regulating H2 O2 production. Mitochondrial outer membrane protein 64 is a potentially efficient candidate to improve BPH and SSB resistance through gene deletion. Why the om64 mutant was resistant to both piercing-sucking and chewing insects via a gene deficiency in mitochondria is discussed.
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Affiliation(s)
- Hui-Min Guo
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hai-Chao Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shi-Rong Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xue-Xia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Shanghai, 200032, China
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Kersten B, Leite Montalvão AP, Hoenicka H, Vettori C, Paffetti D, Fladung M. Sequencing of two transgenic early-flowering poplar lines confirmed vector-free single-locus T-DNA integration. Transgenic Res 2020; 29:321-337. [PMID: 32356192 PMCID: PMC7283205 DOI: 10.1007/s11248-020-00203-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/18/2020] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing (NGS) approaches are attractive alternatives to the PCR-based characterisation of genetically modified plants for safety assessment and labelling since NGS is highly sensitive to the detection of T-DNA inserts as well as vector backbone sequences in transgenic plants. In this study, two independent transgenic male Populus tremula lines, T193-2 and T195-1, both carrying the FLOWERING LOCUS T gene from Arabidopsis thaliana under control of a heat-inducible promoter (pHSP::AtFT) and the non-transgenic control clone W52, were further characterised by NGS and third-generation sequencing. The results support previous findings that the T-DNA was hemizygously inserted in one genomic locus of each line. However, the T-DNA insertions consist of conglomerations of one or two T-DNA copies together with a small T-DNA fragment without AtFT parts. Based on NGS data, no additional T-DNA splinters or vector backbone sequences could be identified in the genome of the two transgenic lines. Seedlings derived from crosses between the pHSP::AtFT transgenic male parents and female wild type plants are therefore expected to be T-DNA splinter or vector backbone free. Thus, PCR analyses amplifying a partial T-DNA fragment with AtFT-specific primers are sufficient to determine whether the seedlings are transgenic or not. An analysis of 72 second generation-seedlings clearly showed that about 50% of them still reveal the presence of the T-DNA, confirming data already published. To prove if unanticipated genomic changes were induced by T-DNA integration, extended future studies using long-range sequencing technologies are required once a suitable chromosome-level P. tremula reference genome sequence is available.
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Affiliation(s)
- Birgit Kersten
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany.
| | | | - Hans Hoenicka
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany
| | - Cristina Vettori
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry, Agricultural Genetics Section, University of Florence, P. le delle Cascine 18, 50144, Florence, Italy
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany.
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Tan C, Zhang XQ, Wang Y, Wu D, Bellgard MI, Xu Y, Shu X, Zhou G, Li C. Characterization of genome-wide variations induced by gamma-ray radiation in barley using RNA-Seq. BMC Genomics 2019; 20:783. [PMID: 31664908 PMCID: PMC6819550 DOI: 10.1186/s12864-019-6182-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 10/11/2019] [Indexed: 11/30/2022] Open
Abstract
Background Artificial mutagenesis not only provides a new approach to increase the diversity of desirable traits for breeding new varieties but are also beneficial for characterizing the genetic basis of functional genes. In recent decades, many mutation genes have been identified which are responsible for phenotype changes in mutants in various species including Arabidopsis and rice. However, the mutation feature in induced mutants and the underlying mechanisms of various types of artificial mutagenesis remain unclear. Results In this study, we adopted a transcriptome sequencing strategy to characterize mutations in coding regions in a barley dwarf mutant induced by gamma-ray radiation. We detected 1193 genetic mutations in gene transcription regions introduced by gamma-ray radiation. Interestingly, up to 97% of the gamma irradiation mutations were concentrated in certain regions in chromosome 5H and chromosome 7H. Of the 26,745 expressed genes, 140 were affected by gamma-ray radiation; their biological functions included cellular and metabolic processes. Conclusion Our results indicate that mutations induced by gamma-ray radiation are not evenly distributed across the whole genome but located in several concentrated regions. Our study provides an overview of the feature of genetic mutations and the genes affected by gamma-ray radiation, which should contribute to a deeper understanding of the mechanisms of radiation mutation and their application in gene function analysis.
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Affiliation(s)
- Cong Tan
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia.,Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
| | - Yin Wang
- IAEA Collaborating Center, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029, China
| | - Dianxin Wu
- IAEA Collaborating Center, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029, China
| | - Matthew I Bellgard
- eResearch Office, Queensland University of Technology, Brisbane, 4000, Australia
| | - Yanhao Xu
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Xiaoli Shu
- eResearch Office, Queensland University of Technology, Brisbane, 4000, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia.,Western Australia Department of Primary Industry and Regional Development, South Perth, WA, 6151, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia. .,IAEA Collaborating Center, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029, China. .,Western Australia Department of Primary Industry and Regional Development, South Perth, WA, 6151, Australia.
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Gang H, Liu G, Zhang M, Zhao Y, Jiang J, Chen S. Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant. BMC Genomics 2019; 20:311. [PMID: 31014254 PMCID: PMC6480916 DOI: 10.1186/s12864-019-5636-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/24/2019] [Indexed: 11/29/2022] Open
Abstract
Background Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in plant research. T-DNA integration in plants is complex and still largely unknown. In this work, we reported that multiple T-DNA fragments caused chromosomal translocation and deletion in a birch (Betula platyphylla × B. pendula) T-DNA mutant yl. Results We performed PacBio genome resequencing for yl and the result revealed that two ends of a T-DNA can be integrated into plant genome independently because the two ends can be linked to different chromosomes and cause chromosomal translocation. We also found that these T-DNA were connected into tandem fragment regardless of direction before integrating into plant genome. In addition, the integration of T-DNA in yl genome also caused several chromosomal fragments deletion. We then summarized three cases for T-DNA integration model in the yl genome. (1) A T-DNA fragment is linked to the two ends of a double-stranded break (DSB); (2) Only one end of a T-DNA fragment is linked to a DSB; (3) A T-DNA fragment is linked to the ends of different DSBs. All the observations in the yl genome supported the DSB repair model. Conclusions In this study, we showed a comprehensive genome analysis of a T-DNA mutant and provide a new insight into T-DNA integration in plants. These findings would be helpful for the analysis of T-DNA mutants with special phenotypes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5636-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huixin Gang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Manman Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yuming Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Ni S, Li Z, Ying J, Zhang J, Chen H. Decreased Spikelets 4 Encoding a Novel Tetratricopeptide Repeat Domain-Containing Protein Is Involved in DNA Repair and Spikelet Number Determination in Rice. Genes (Basel) 2019; 10:genes10030214. [PMID: 30871267 PMCID: PMC6471630 DOI: 10.3390/genes10030214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Spikelet number per panicle is a determinative factor of rice yield. DNA repair epigenetically alters the DNA accessibility, which can eventually regulate the transcription of the target genes. However, what and how DNA repair genes are related to rice spikelet development remains unknown. Here, we report the map-based cloning of a novel spikelet number gene DES4 encoding a tetratricopeptide domain-containing protein. DES4 is a close ortholog of Arabidopsis BRU1, which is functionally related to axillary meristem development. A single base pair deletion in the last exon of DES4 caused a premature stop of the resulting protein. The des4 mutant exhibited dwarf, reduced tiller, and spikelet numbers phenotypes, as well as hypersensitivity to genotoxic stresses, suggesting its essential role in DNA repair. DES4 is predominantly expressed in young panicles and axillary meristems, and DES4 protein is localized in nucleus. A set of DNA repair genes such as cyclins, KUs (KD subunits) and recombinases were differentially regulated in des4. Meanwhile, rice spikelet number genes LAX1, LAX2, and MOC1 were significantly down-regulated in des4. In morphology, des4 showed more severe reduction of spikelet numbers than lax1, lax2, and moc1, suggesting that DES4 may work upstream of the three genes.
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Affiliation(s)
- Shen Ni
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Zongzhu Li
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA.
| | - Jiancheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Hongqi Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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13
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Tong X, Wang Y, Sun A, Bello BK, Ni S, Zhang J. Notched Belly Grain 4, a Novel Allele of Dwarf 11, Regulates Grain Shape and Seed Germination in Rice (Oryza sativa L.). Int J Mol Sci 2018; 19:ijms19124069. [PMID: 30558382 PMCID: PMC6321642 DOI: 10.3390/ijms19124069] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
Notched belly grain (NBG) is a type of deformed grain shape that has been associated with inferior appearance and tastes in rice. NBG is coordinated by both environments and genetics. In this study, we report on the first map-based cloning of an NBG gene on chromosome 4, denoted NBG4, which is a novel allele of Dwarf 11 encoding a cytochrome P450 (CYP724B1) involved in brassinosteroid (BR) biosynthesis. A 10-bp deletion in the 7th exon knocked down the level of the NBG4 transcript and shifted the reading frame of the resulting protein. In addition to the dwarf and clustered panicle as previously reported in the allelic mutants, nbg4 grains also displayed retarded germination and NBG due to the physical constraint of deformed hulls caused by abnormal hull elongation. NBG4 is constitutively expressed with the highest level of expression in immature inflorescences. In all, 2294 genes were differentially expressed in nbg4 and wild-type (WT), and evidence is presented that NBG4 regulates OsPPS-2, OsPRA2, OsYUCCA1, sped1-D, and Dwarf that play critical roles in determining plant architecture, panicle development, and seed germination. This study demonstrated that NBG4 is a key node in the brassinosteroid-mediated regulation of rice grain shape.
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Affiliation(s)
- Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Aiqun Sun
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Babatunde Kazeem Bello
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Shen Ni
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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14
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Li Z, Wang Y, Bello BK, Ajadi AA, Tong X, Chang Y, Zhang J. Construction of a Quantitative Acetylomic Tissue Atlas in Rice ( Oryza sativa L.). Molecules 2018; 23:molecules23112843. [PMID: 30388832 PMCID: PMC6278296 DOI: 10.3390/molecules23112843] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues.
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Affiliation(s)
- Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Babatunde Kazeem Bello
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Abolore Adijat Ajadi
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yuxiao Chang
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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15
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Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM. Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. eLife 2018. [PMID: 29521624 PMCID: PMC5922974 DOI: 10.7554/elife.32110] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi. The fungus Rhodosporidium toruloides can grow on substances extracted from plant matter that is inedible to humans such as corn stalks, wood pulp, and grasses. Under some growth conditions, the fungus can accumulate massive stores of hydrocarbon-rich fats and pigments. A community of scientists and engineers has begun genetically modifying R. toruloides to convert these naturally produced fats and pigments into fuels, chemicals and medicines. These could form sustainable replacements for products made from petroleum or harvested from threatened animal and plant species. Fungi, plants, animals and other eukaryotes store fat in specialized compartments called lipid droplets. The genes that control the metabolism – the production, use and storage – of fat in lipid bodies have been studied in certain eukaryotes, including species of yeast. However, R. toruloides is only distantly related to the most well-studied of these species. This means that we cannot be certain that a gene will play the same role in R. toruloides as in those species. To assemble the most comprehensive list possible of the genes in R. toruloides that affect the production, use, or storage of fat in lipid bodies, Coradetti, Pinel et al. constructed a population of hundreds of thousands of mutant fungal strains, each with its own unique DNA ‘barcode’. The effects that mutations in over 6,000 genes had on growth and fat accumulation in these fungi were measured simultaneously in several experiments. This general approach is not new, but technical limitations had, until now, restricted its use in fungi to a few species. Coradetti, Pinel et al. identified hundreds of genes that affected the ability of R. toruloides to metabolise fat. Many of these genes were related to genes with known roles in fat metabolism in other eukaryotes. Other genes are involved in different cell processes, such as the recycling of waste products in the cell. Their identification adds weight to the view that the links between these cellular processes and fat metabolism are deep and widespread amongst eukaryotes. Finally, some of the genes identified by Coradetti, Pinel et al. are not closely related to any well-studied genes. Further study of these genes could help us to understand why R. toruloides can accumulate much larger amounts of fat than most other fungi. The methods developed by Coradetti, Pinel et al. should be possible to implement in many species of fungi. As a result these techniques may eventually contribute to the development of new treatments for human fungal diseases, the protection of important food crops, and a deeper understanding of the roles various fungi play in the broader ecosystem.
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Affiliation(s)
| | - Dominic Pinel
- Energy Biosciences Institute, Berkeley, United States
| | | | - Masakazu Ito
- Energy Biosciences Institute, Berkeley, United States
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, United States.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, United States
| | - Ya-Fang Cheng
- Energy Biosciences Institute, Berkeley, United States
| | - Stefan Bauer
- Energy Biosciences Institute, Berkeley, United States
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel B Brem
- The Buck Institute for Research on Aging, Novato, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Adam P Arkin
- Energy Biosciences Institute, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Jeffrey M Skerker
- Energy Biosciences Institute, Berkeley, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
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16
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The Mechanism of T-DNA Integration: Some Major Unresolved Questions. Curr Top Microbiol Immunol 2018; 418:287-317. [DOI: 10.1007/82_2018_98] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Wang Y, Lin H, Tong X, Hou Y, Chang Y, Zhang J. DNA demethylation activates genes in seed maternal integument development in rice (Oryza sativa L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 120:169-178. [PMID: 29031162 DOI: 10.1016/j.plaphy.2017.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/11/2017] [Accepted: 09/24/2017] [Indexed: 06/07/2023]
Abstract
DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development. Bisulfite sanger sequencing and qRT-PCR of six differentially methylated genes revealed extensive occurrence of DNA hypomethylation triggered by double fertilization at IAP compared with IBP, suggesting that DNA demethylation might be a key mechanism to activate numerous maternal controlling genes. These results presented here not only greatly expanded the rice methylome dataset, but also shed novel insight into the regulatory roles of DNA methylation in rice seed maternal integument development.
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Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Haiyan Lin
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaohong Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yuxuan Hou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yuxiao Chang
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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18
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Pérez‐Martín F, Yuste‐Lisbona FJ, Pineda B, Angarita‐Díaz MP, García‐Sogo B, Antón T, Sánchez S, Giménez E, Atarés A, Fernández‐Lozano A, Ortíz‐Atienza A, García‐Alcázar M, Castañeda L, Fonseca R, Capel C, Goergen G, Sánchez J, Quispe JL, Capel J, Angosto T, Moreno V, Lozano R. A collection of enhancer trap insertional mutants for functional genomics in tomato. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1439-1452. [PMID: 28317264 PMCID: PMC5633825 DOI: 10.1111/pbi.12728] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/03/2017] [Accepted: 03/15/2017] [Indexed: 05/06/2023]
Abstract
With the completion of genome sequencing projects, the next challenge is to close the gap between gene annotation and gene functional assignment. Genomic tools to identify gene functions are based on the analysis of phenotypic variations between a wild type and its mutant; hence, mutant collections are a valuable resource. In this sense, T-DNA collections allow for an easy and straightforward identification of the tagged gene, serving as the basis of both forward and reverse genetic strategies. This study reports on the phenotypic and molecular characterization of an enhancer trap T-DNA collection in tomato (Solanum lycopersicum L.), which has been produced by Agrobacterium-mediated transformation using a binary vector bearing a minimal promoter fused to the uidA reporter gene. Two genes have been isolated from different T-DNA mutants, one of these genes codes for a UTP-glucose-1-phosphate uridylyltransferase involved in programmed cell death and leaf development, which means a novel gene function reported in tomato. Together, our results support that enhancer trapping is a powerful tool to identify novel genes and regulatory elements in tomato and that this T-DNA mutant collection represents a highly valuable resource for functional analyses in this fleshy-fruited model species.
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Affiliation(s)
- Fernando Pérez‐Martín
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | | | - Benito Pineda
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - María Pilar Angarita‐Díaz
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Begoña García‐Sogo
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Teresa Antón
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Sibilla Sánchez
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Estela Giménez
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Alejandro Atarés
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Antonia Fernández‐Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Ana Ortíz‐Atienza
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Manuel García‐Alcázar
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Laura Castañeda
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Rocío Fonseca
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Geraldine Goergen
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Jorge Sánchez
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Jorge L. Quispe
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Juan Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Vicente Moreno
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
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19
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Wang Y, Tong X, Qiu J, Li Z, Zhao J, Hou Y, Tang L, Zhang J. A phosphoproteomic landscape of rice (Oryza sativa) tissues. PHYSIOLOGIA PLANTARUM 2017; 160:458-475. [PMID: 28382632 DOI: 10.1111/ppl.12574] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Protein phosphorylation is an important posttranslational modification that regulates various plant developmental processes. Here, we report a comprehensive, quantitative phosphoproteomic profile of six rice tissues, including callus, leaf, root, shoot meristem, young panicle and mature panicle from Nipponbare by employing a mass spectrometry (MS)-based, label-free approach. A total of 7171 unique phosphorylation sites in 4792 phosphopeptides from 2657 phosphoproteins were identified, of which 4613 peptides were differentially phosphorylated (DP) among the tissues. Motif-X analysis revealed eight significantly enriched motifs, such as [sP], [Rxxs] and [tP] from the rice phosphosites. Hierarchical clustering analysis divided the DP peptides into 63 subgroups, which showed divergent spatial-phosphorylation patterns among tissues. These clustered proteins are functionally related to nutrition uptake in roots, photosynthesis in leaves and tissue differentiation in panicles. Phosphorylations were specific in the tissues where the target proteins execute their functions, suggesting that phosphorylation might be a key mechanism to regulate the protein activity in different tissues. This study greatly expands the rice phosphoproteomic dataset, and also offers insight into the regulatory roles of phosphorylation in tissue development and functions.
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Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaohong Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jiehua Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhiyong Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Juan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yuxuan Hou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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20
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A Quantitative Acetylomic Analysis of Early Seed Development in Rice (Oryza sativa L.). Int J Mol Sci 2017; 18:ijms18071376. [PMID: 28654018 PMCID: PMC5535869 DOI: 10.3390/ijms18071376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 11/20/2022] Open
Abstract
PKA (protein lysine acetylation) is a critical post-translational modification that regulates various developmental processes, including seed development. However, the acetylation events and dynamics on a proteomic scale in this process remain largely unknown, especially in rice early seed development. We report the first quantitative acetylproteomic study focused on rice early seed development by employing a mass spectral-based (MS-based), label-free approach. A total of 1817 acetylsites on 1688 acetylpeptides from 972 acetylproteins were identified in pistils and seeds at three and seven days after pollination, including 268 acetyproteins differentially acetylated among the three stages. Motif-X analysis revealed that six significantly enriched motifs, such as (DxkK), (kH) and (kY) around the acetylsites of the identified rice seed acetylproteins. Differentially acetylated proteins among the three stages, including adenosine diphosphate (ADP) -glucose pyrophosphorylases (AGPs), PDIL1-1 (protein disulfide isomerase like 1-1), hexokinases, pyruvate dehydrogenase complex (PDC) and numerous other regulators that are extensively involved in the starch and sucrose metabolism, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle and photosynthesis pathways during early seed development. This study greatly expanded the rice acetylome dataset, and shed novel insight into the regulatory roles of PKA in rice early seed development.
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21
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Chen T, Wu H, Wu J, Fan X, Li X, Lin Y. Absence of OsβCA1 causes a CO 2 deficit and affects leaf photosynthesis and the stomatal response to CO 2 in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:344-357. [PMID: 28142196 DOI: 10.1111/tpj.13497] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 05/07/2023]
Abstract
Plants always adjust the opening of stomatal pores to adapt to the environment, for example CO2 concentration ([CO2 ]), humidity and temperature. Low [CO2 ] will trigger the opening of stomatal pores to absorb extra CO2 . However, little is known about how CO2 supply affects the carbon fixation and opening of stomatal pores in rice. Here, a chloroplast-located gene coding for β-carbonic anhydrase (βCA) was found to be involved in carbon assimilation and the CO2 -mediated stomatal pore response in rice. OsβCA1 was constitutively expressed in all tissues and its transcripts were induced by high [CO2 ] in leaves. Both T-DNA mutant and RNA interference lines showed phenotypes of lower biomass and CA activities. Knockout of OsβCA1 obviously decreased photosynthetic capacity, as demonstrated by the increased CO2 compensation point and decreased light saturation point in the mutant, while knockout increased the opening ratio of stomatal pores and the rate of water loss. Moreover, the mutant showed a delayed response to low [CO2 ], and stomatal pores could not be closed to the same degree as those of wild type even though the stomatal pores could rapidly respond to high [CO2 ]. Genome-wide gene expression analysis via RNA sequencing demonstrated that the transcript abundance of genes related to Rubisco, photosystem compounds and the opening of stomatal pores was globally upregulated in the mutant. Taken together, the inadequate CO2 supply caused by the absence of OsβCA1 reduces photosynthetic efficiency, triggers the opening of stomatal pores and finally decreases their sensitivity to CO2 fluctuation.
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Affiliation(s)
- Taiyu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Jiemin Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Xiaolei Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
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22
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Ying J, Zhao J, Hou Y, Wang Y, Qiu J, Li Z, Tong X, Shi Z, Zhu J, Zhang J. Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos. PLoS One 2017; 12:e0173853. [PMID: 28328971 PMCID: PMC5362090 DOI: 10.1371/journal.pone.0173853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/28/2017] [Indexed: 11/19/2022] Open
Abstract
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered. Inspection of the motifs and sequence structures involved suggested that all the glycosites were concentrated within [NxS/T] motif, while 82.3% of them were in a coil structure. N-glycosylation preferentially occurred on proteins with glycoside hydrolase activities, which were significantly enriched in the starch and sucrose metabolism pathway, suggesting that N-glycosylation is involved in embryo germination by regulating carbohydrate metabolism. Notably, protein-protein interaction analysis revealed a network with several Brassinosteroids signaling proteins, including XIAO and other BR-responsive proteins, implying that glycosylation-mediated Brassinosteroids signaling may be a key mechanism regulating rice embryo germination. In summary, this study expanded our knowledge of protein glycosylation in rice, and provided novel insight into the PTM regulation in rice seed germination.
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Affiliation(s)
- Jiezheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Juan Zhao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | | | - Jun Zhu
- Jingjie PTM-Biolabs, Hangzhou, P.R. China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
- * E-mail:
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23
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Li X, Guo K, Zhu X, Chen P, Li Y, Xie G, Wang L, Wang Y, Persson S, Peng L. Domestication of rice has reduced the occurrence of transposable elements within gene coding regions. BMC Genomics 2017; 18:55. [PMID: 28068923 PMCID: PMC5223533 DOI: 10.1186/s12864-016-3454-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/22/2016] [Indexed: 11/19/2022] Open
Abstract
Background Transposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are thus proposed as an ideal model to study TEs roles in the context of plant genome evolution. As TEs may contribute to improved rice growth and grain quality, it is of pivotal significance for worldwide food security and biomass production. Results We analyzed three cultivated rice species and their closest five wild relatives for distribution and content of TEs in their genomes. Despite that the three cultivar rice species contained similar copies and more total TEs, their genomes contained much longer TEs as compared to their wild relatives. Notably, TEs were largely depleted from genomic regions that corresponded to genes in the cultivated species, while this was not the case for their wild relatives. Gene ontology and gene homology analyses revealed that while certain genes contained TEs in all the wild species, the closest homologs in the cultivated species were devoid of them. This distribution of TEs is surprising as the cultivated species are more distantly related to each other as compared to their closest wild relative. Hence, cultivated rice species have more similar TE distributions among their genes as compared to their closest wild relatives. We, furthermore, exemplify how genes that are conferring important rice traits can be regulated by TE associations. Conclusions This study demonstrate that the cultivation of rice has led to distinct genomic distribution of TEs, and that certain rice traits are closely associated with TE distribution patterns. Hence, the results provide means to better understand TE-dependent rice traits and the potential to genetically engineer rice for better performance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3454-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xukai Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Kai Guo
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Xiaobo Zhu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Ying Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Guosheng Xie
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Lingqiang Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Staffan Persson
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,School of Biosciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
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24
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Hou Y, Qiu J, Wang Y, Li Z, Zhao J, Tong X, Lin H, Zhang J. A Quantitative Proteomic Analysis of Brassinosteroid-induced Protein Phosphorylation in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:514. [PMID: 28439285 PMCID: PMC5383725 DOI: 10.3389/fpls.2017.00514] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 03/23/2017] [Indexed: 05/21/2023]
Abstract
The group of polyhydroxysteroid phytohormones referred to as the brassinosteroids (BRs) is known to act on plant development and the stress response. BR signal transduction relies largely on protein phosphorylation. By employing a label-free, MS (Mass Spectrometry)-based phosphoproteomic approach, we report here the largest profiling of 4,034 phosphosites on 1,900 phosphoproteins from rice young seedlings and their dynamic response to BR. 1,821 proteins, including kinases, transcription factors and core components of BR and other hormone signaling pathways, were found to be differentially phosphorylated during the BR treatment. A Western blot analysis verified the differential phosphorylation of five of these proteins, implying that the MS-based phosphoproteomic data were robust. It is proposed that the dephosphorylation of gibberellin (GA) signaling components could represent an important mechanism for the BR-regulated antagonism to GA, and that BR influences the plant architecture of rice by regulating cellulose synthesis via phosphorylation.
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Affiliation(s)
- Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Juan Zhao
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Haiyan Lin
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen, China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
- *Correspondence: Jian Zhang,
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25
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Zhao J, Yang Y, Yang D, Cheng Y, Jiao M, Zhan G, Zhang H, Wang J, Zhou K, Huang L, Kang Z. Characterization and Genetic Analysis of Rice Mutant crr1 Exhibiting Compromised Non-host Resistance to Puccinia striiformis f. sp. tritici ( Pst). FRONTIERS IN PLANT SCIENCE 2016; 7:1822. [PMID: 27965705 PMCID: PMC5127839 DOI: 10.3389/fpls.2016.01822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/18/2016] [Indexed: 05/12/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat in China. Rapid change to virulence following release of resistant cultivars necessitates ongoing discovery and exploitation of new resistance resources. Considerable effort has been directed at non-host resistance (NHR) which is believed to be durable. In the present study we identified rice mutant crr1 (compromised resistance to rust 1) that exhibited compromised NHR to Pst. Compared with wild type rice variety Nipponbare, crr1 mutant displayed a threefold increase in penetration rate by Pst, and enhanced hyphal growth. The pathogen also developed haustoria in crr1 mesophyll cells, but failed to sporulate. The response to the adapted rice pathogen Magnaporthe oryzae was unchanged in crr1 relative to the wild type. Several defense-related genes involved in the SA- and JA-mediated defense pathways response and in phytoalexin synthesis (such as OsPR1a, OsLOX1, and OsCPS4) were more rapidly and strongly induced in infected crr1 leaves than in the wild type, suggesting that other layers of defense are still in effect. Genetic analysis and mapping located the mutant loci at a region between markers ID14 and RM25792, which cover about 290 kb genome sequence on chromosome 10. Further fine mapping and cloning of the locus should provide further insights into NHR to rust fungi in rice, and may reveal new strategies for improving rust resistance in wheat.
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Affiliation(s)
- Jing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Yuheng Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Donghe Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Yulin Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Min Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Hongchang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F UniversityYangling, China
| | - Junyi Wang
- Shaanxi Rice Research Institute, Hanzhong Agricultural Science InstituteHanzhong, China
| | - Kai Zhou
- Shaanxi Rice Research Institute, Hanzhong Agricultural Science InstituteHanzhong, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
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26
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Dong H, Zhao H, Xie W, Han Z, Li G, Yao W, Bai X, Hu Y, Guo Z, Lu K, Yang L, Xing Y. A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars. PLoS Genet 2016; 12:e1006412. [PMID: 27814357 PMCID: PMC5096673 DOI: 10.1371/journal.pgen.1006412] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 10/07/2016] [Indexed: 01/09/2023] Open
Abstract
Tiller angle is one of the most important components of the ideal plant architecture that can greatly enhance rice grain yield. Understanding the genetic basis of tiller angle and mining favorable alleles will be helpful for breeding new plant-type varieties. Here, we performed genome-wide association studies (GWAS) to identify genes controlling tiller angle using 529 diverse accessions of Oryza sativa including 295 indica and 156 japonica accessions in two environments. We identified 7 common quantitative trait loci (QTLs), including the previously reported major gene Tiller Angle Control 1 (TAC1), in the two environments, 10 and 13 unique QTLs in Hainan and Wuhan, respectively. More QTLs were identified in indica than in japonica, and three major QTLs (qTA3, qTA1b/DWARF2 (D2) and qTA9c/TAC1) were fixed in japonica but segregating in indica, which explained the wider variation observed in indica compared with that in japonica. No common QTLs were identified between the indica and japonica subpopulations. Mutant analysis for the candidate gene of qTA3 on chromosome 3 indicated a novel gene, Tiller Angle Control 3 (TAC3), encoding a conserved hypothetical protein controlling tiller angle. TAC3 is preferentially expressed in the tiller base. The ebisu dwarf (d2) mutant exhibited a decreased tiller angle, in addition to its previously described abnormal phenotype. A nucleotide diversity analysis revealed that TAC3, D2 and TAC1 have been subjected to selection during japonica domestication. A haplotype analysis identified favorable alleles of TAC3, D2 and TAC1, which may be used for breeding plants with an ideal architecture. In conclusion, there is a diverse genetic basis for tiller angle between the two subpopulations, and it is the novel gene TAC3 together with TAC1, D2, and other newly identified genes in this study that controls tiller angle in rice cultivars. Tiller angle is the key component of plant architecture that greatly affect grain yield. However, few tiller angle-related genes that can be used for improving rice plant architecture have been isolated based on natural variation. Here, we identified 7 common tiller angle-related QTLs by a genome-wide association study, including the previously reported major gene TAC1, in two environments in the 529 diverse rice accessions and dozens of QTLs specially identified in one environment. Two QTLs were validated by mutant analysis: A novel gene TAC3, encoding a conserved hypothetical protein and preferentially expressing in the tiller base, was the candidate gene of qTA3; d2 mutant exhibited a decreased tiller angle, in addition to its previously described abnormal phenotype. A haplotype analysis identified favorable alleles of TAC3, D2 and TAC1 in indica, which may be used for breeding plants with an ideal architecture, while they were all subjected to selection and fixed in japonica. In conclusion, there is a diverse genetic basis for tiller angle between the two subpopulations, and it is the novel gene TAC3, together with TAC1 and D2 that greatly controls tiller angle in rice cultivars.
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Affiliation(s)
- Haijiao Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Wen Yao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Xufeng Bai
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Zilong Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Kai Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Lin Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
- Hubei Collaborative Innovation Center for Grain Industry, China
- * E-mail:
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27
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Xuan YH, Kim CM, Je BI, Liu JM, Li TY, Lee GS, Kim TH, Han CD. Transposon Ds-Mediated Insertional Mutagenesis in Rice (Oryza sativa). CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:466-487. [PMID: 31725960 DOI: 10.1002/cppb.20030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Rice (Oryza sativa) is the most important consumed staple food for a large and diverse population worldwide. Since databases of genomic sequences became available, functional genomics and genetic manipulations have been widely practiced in rice research communities. Insertional mutants are the most common genetic materials utilized to analyze gene function. To mutagenize rice genomes, we exploited the transpositional activity of an Activator/Dissociation (Ac/Ds) system in rice. To mobilize Ds in rice genomes, a maize Ac cDNA was expressed under the CaMV35S promoter, and a gene trap Ds was utilized to detect expression of host genes via the reporter gene GUS. Conventional transposon-mediated gene-tagging systems rely on genetic crossing and selection markers. Furthermore, the activities of transposases have to be monitored. By taking advantage of the fact that Ds becomes highly active during tissue culture, a plant regeneration system employing tissue culture was employed to generate a large Ds transposant population in rice. This system overcomes the requirement for markers and the monitoring of Ac activity. In the regenerated populations, more than 70% of the plant lines contained independent Ds insertions and 12% expressed GUS at seedling stages. This protocol describes the method for producing a Ds-mediated insertional population via tissue culture regeneration systems. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Chul Min Kim
- Division of Applied Life Science (BK21 program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Byoung Il Je
- Division of Applied Life Science (BK21 program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Jing Miao Liu
- Division of Applied Life Science (BK21 program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Tian Ya Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Gang-Seob Lee
- Biosafty Division, Department of Agricultural Biotechnology, National Institute of Agricultural Science (NIAS), RDA, Jeonju, Korea
| | - Tae-Ho Kim
- Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Science (NIAS), RDA, Jeonju, Korea
| | - Chang-Deok Han
- Division of Applied Life Science (BK21 program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
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28
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Li Z, Tang L, Qiu J, Zhang W, Wang Y, Tong X, Wei X, Hou Y, Zhang J. Serine carboxypeptidase 46 Regulates Grain Filling and Seed Germination in Rice (Oryza sativa L.). PLoS One 2016; 11:e0159737. [PMID: 27448032 PMCID: PMC4957776 DOI: 10.1371/journal.pone.0159737] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/07/2016] [Indexed: 11/19/2022] Open
Abstract
Serine carboxypeptidase (SCP) is one of the largest groups of enzymes catalyzing proteolysis for functional protein maturation. To date, little is known about the function of SCPs in rice. In this study, we present a comprehensive analysis of the gene structure and expression profile of 59 rice SCPs. SCP46 is dominantly expressed in developing seeds, particularly in embryo, endosperm and aleurone layers, and could be induced by ABA. Functional characterization revealed that knock-down of SCP46 resulted in smaller grain size and enhanced seed germination. Furthermore, scp46 seed germination became less sensitive to the ABA inhibition than the Wild-type did; suggesting SCP46 is involved in ABA signaling. As indicated by RNA-seq and qRT-PCR analysis, numerous grain filling and seed dormancy related genes, such as SP, VP1 and AGPs were down-regulated in scp46. Yeast-two-hybrid assay also showed that SCP46 interacts with another ABA-inducible protein DI19-1. Taken together, we suggested that SCP46 is a master regulator of grain filling and seed germination, possibly via participating in the ABA signaling. The results of this study shed novel light into the roles of SCPs in rice.
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Affiliation(s)
- Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, P.R. China
| | - Liqun Tang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, P.R. China
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, P.R. China
| | - Wen Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, P.R. China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, P.R. China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, P.R. China
| | - Xiangjin Wei
- China National Rice Research Institute, Hangzhou, 311400, P.R. China
| | - Yuxuan Hou
- China National Rice Research Institute, Hangzhou, 311400, P.R. China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, P.R. China
- * E-mail:
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29
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Stephan BI, Alvarez Crespo MC, Kemppainen MJ, Pardo AG. Agrobacterium-mediated insertional mutagenesis in the mycorrhizal fungus Laccaria bicolor. Curr Genet 2016; 63:215-227. [PMID: 27387518 DOI: 10.1007/s00294-016-0627-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 11/24/2022]
Abstract
Agrobacterium-mediated gene transfer (AMT) is extensively employed as a tool in fungal functional genomics and accordingly, in previous studies we used AMT on a dikaryotic strain of the ectomycorrhizal basidiomycete Laccaria bicolor. The interest in this fungus derives from its capacity to establish a symbiosis with tree roots, thereby playing a major role in nutrient cycling of forest ecosystems. The ectomycorrhizal symbiosis is a highly complex interaction involving many genes from both partners. To advance in the functional characterization of fungal genes, AMT was used on a monokaryotic L. bicolor. A collection of over 1200 transgenic strains was produced, of which 200 randomly selected strains were analyzed for their genomic T-DNA insertion patterns. By means of insertional mutagenesis, a number of transgenic strains were obtained displaying differential growth features. Moreover, mating with a compatible strain resulted in dikaryons that retained altered phenotypic features of the transgenic monokaryon. The analysis of the T-DNA integration pattern revealed mostly similar results to those reported in earlier studies, confirming the usefulness of AMT on different genetic backgrounds of L. bicolor. Taken together, our studies display the great versatility and potentiality of AMT as a tool for the genetic characterization of L. bicolor.
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Affiliation(s)
- B I Stephan
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Consejo Nacional de Investigaciones Científicas y Técnicas, Roque Saenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - M C Alvarez Crespo
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Consejo Nacional de Investigaciones Científicas y Técnicas, Roque Saenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - M J Kemppainen
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Consejo Nacional de Investigaciones Científicas y Técnicas, Roque Saenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - A G Pardo
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Consejo Nacional de Investigaciones Científicas y Técnicas, Roque Saenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina.
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30
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Qiu J, Hou Y, Tong X, Wang Y, Lin H, Liu Q, Zhang W, Li Z, Nallamilli BR, Zhang J. Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2016; 90:249-265. [PMID: 26613898 DOI: 10.1007/s11103-015-0410-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 11/23/2015] [Indexed: 06/05/2023]
Abstract
Rice (Oryza sativa L.) seed serves as a major food source for over half of the global population. Though it has been long recognized that phosphorylation plays an essential role in rice seed development, the phosphorylation events and dynamics in this process remain largely unknown so far. Here, we report the first large scale identification of rice seed phosphoproteins and phosphosites by using a quantitative phosphoproteomic approach. Thorough proteomic studies in pistils and seeds at 3, 7 days after pollination resulted in the successful identification of 3885, 4313 and 4135 phosphopeptides respectively. A total of 2487 proteins were differentially phosphorylated among the three stages, including Kip related protein 1, Rice basic leucine zipper factor 1, Rice prolamin box binding factor and numerous other master regulators of rice seed development. Moreover, differentially phosphorylated proteins may be extensively involved in the biosynthesis and signaling pathways of phytohormones such as auxin, gibberellin, abscisic acid and brassinosteroid. Our results strongly indicated that protein phosphorylation is a key mechanism regulating cell proliferation and enlargement, phytohormone biosynthesis and signaling, grain filling and grain quality during rice seed development. Overall, the current study enhanced our understanding of the rice phosphoproteome and shed novel insight into the regulatory mechanism of rice seed development.
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Affiliation(s)
- Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Haiyan Lin
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Qing Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Wen Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Babi R Nallamilli
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China.
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Hou Y, Wang L, Wang L, Liu L, Li L, Sun L, Rao Q, Zhang J, Huang S. JMJ704 positively regulates rice defense response against Xanthomonas oryzae pv. oryzae infection via reducing H3K4me2/3 associated with negative disease resistance regulators. BMC PLANT BIOLOGY 2015; 15:286. [PMID: 26646110 PMCID: PMC4673860 DOI: 10.1186/s12870-015-0674-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/03/2015] [Indexed: 05/17/2023]
Abstract
BACKGROUND Jumonji C (JmjC) domain-containing proteins are a group of functionally conserved histone lysine demethylases in Eukaryotes. Growing evidences have shown that JmjCs epigenetically regulate various biological processes in plants. However, their roles in plant biotic stress, especially in rice bacterial blight resistance have been barely studied so far. RESULTS In this study, we found that the global di- and tri-methylation levels on multiple lysine sites of histone three were dramatically altered after being infected by bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). Xoo infection induced the transcription of 15 JmjCs, suggesting these JmjCs are involved in rice bacterial blight defense. Further functional characterization of JmjC mutants revealed that JMJ704 is a positive regulator of rice bacterial blight resistance as the jmj704 became more susceptible to Xoo than the wild-type. In jmj704, the H3K4me2/3 levels were significantly increased; suggesting JMJ704 may be involved in H3K4me2/3 demethylation. Moreover, JMJ704 suppressed the transcription of the rice defense negative regulator genes, such as NRR, OsWRKY62 and Os-11N3, by reducing the activation marks H3K4me2/3 on them. CONCLUSIONS JMJ704 may be a universal switch controlling multiple genes of the bacterial blight resistance pathway. JMJ704 positively regulates rice defense by epigenetically suppressing master negative defense regulators, presenting a novel mechanism distinct from its homolog JMJ705 which also positively regulates rice defense but via activating positive defense regulators.
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Affiliation(s)
- Yuxuan Hou
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Liyuan Wang
- School of Agricultural and Food Science, Zhejiang A & F University, Lin'an, 311300, China.
| | - Ling Wang
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Lianmeng Liu
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Lu Li
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Lei Sun
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Qiong Rao
- School of Agricultural and Food Science, Zhejiang A & F University, Lin'an, 311300, China.
| | - Jian Zhang
- State key lab of rice biology, China National Rice Research Insititute, Hangzhou, 311400, China.
| | - Shiwen Huang
- China National Rice Research Institute, Hangzhou, 311400, China.
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Bourras S, Rouxel T, Meyer M. Agrobacterium tumefaciens Gene Transfer: How a Plant Pathogen Hacks the Nuclei of Plant and Nonplant Organisms. PHYTOPATHOLOGY 2015; 105:1288-1301. [PMID: 26151736 DOI: 10.1094/phyto-12-14-0380-rvw] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Agrobacterium species are soilborne gram-negative bacteria exhibiting predominantly a saprophytic lifestyle. Only a few of these species are capable of parasitic growth on plants, causing either hairy root or crown gall diseases. The core of the infection strategy of pathogenic Agrobacteria is a genetic transformation of the host cell, via stable integration into the host genome of a DNA fragment called T-DNA. This genetic transformation results in oncogenic reprogramming of the host to the benefit of the pathogen. This unique ability of interkingdom DNA transfer was largely used as a tool for genetic engineering. Thus, the artificial host range of Agrobacterium is continuously expanding and includes plant and nonplant organisms. The increasing availability of genomic tools encouraged genome-wide surveys of T-DNA tagged libraries, and the pattern of T-DNA integration in eukaryotic genomes was studied. Therefore, data have been collected in numerous laboratories to attain a better understanding of T-DNA integration mechanisms and potential biases. This review focuses on the intranuclear mechanisms necessary for proper targeting and stable expression of Agrobacterium oncogenic T-DNA in the host cell. More specifically, the role of genome features and the putative involvement of host's transcriptional machinery in relation to the T-DNA integration and effects on gene expression are discussed. Also, the mechanisms underlying T-DNA integration into specific genome compartments is reviewed, and a theoretical model for T-DNA intranuclear targeting is presented.
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Affiliation(s)
- Salim Bourras
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Thierry Rouxel
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Michel Meyer
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
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Huang Z, Lin J, Cheng Z, Xu M, Huang X, Yang Z, Zheng J. Production of dammarane-type sapogenins in rice by expressing the dammarenediol-II synthase gene from Panax ginseng C.A. Mey. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 239:106-14. [PMID: 26398795 DOI: 10.1016/j.plantsci.2015.07.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 07/10/2015] [Accepted: 07/25/2015] [Indexed: 05/06/2023]
Abstract
Ginsenosides are the main active ingredients in Chinese medicinal ginseng; 2,3-oxidosqualene is a precursor metabolite to ginsenosides that is present in rice. Because rice lacks a key rate-limiting enzyme (dammarenediol-II synthase, DS), rice cannot synthesize dammarane-type ginsenosides. In this study, the ginseng (Panax ginseng CA Mey.) DS gene (GenBank: AB265170.1) was transformed into rice using agrobacterium, and 64 rice transgenic plants were produced. The Transfer-DNA (T-DNA) insertion sites in homozygous lines of the T2 generation were determined by using high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR) and differed in all tested lines. One to two copies of the T-DNA were present in each transformant, and real-time PCR and Western blotting showed that the transformed DS gene could be transcribed and highly expressed. High performance liquid chromatography (HPLC) analysis showed that the dammarane-type sapogenin 20(S)-protopanaxadiol (PPD) content was 0.35-0.59 mg/g dw and the dammarane-type sapogenin 20(S)-protopanaxatriol (PPT) content was 0.23-0.43 mg/g dw in the transgenic rice. LC/MS analysis confirmed production of PPD and PPT. These results indicate that a new "ginseng rice" germplasm containing dammarane-type sapogenins has been successfully developed by transforming the ginseng DS gene into rice.
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Affiliation(s)
- Zhiwei Huang
- College of Food Science, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, CangShan District, Fuzhou, Fujian 350002, China; Agricultural Product Quality Institute, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, CangShan District, Fuzhou, Fujian 350002, China.
| | - Juncheng Lin
- Agricultural Product Quality Institute, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, CangShan District, Fuzhou, Fujian 350002, China.
| | - Zuxin Cheng
- Agricultural Product Quality Institute, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, CangShan District, Fuzhou, Fujian 350002, China.
| | - Ming Xu
- Agricultural Product Quality Institute, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, CangShan District, Fuzhou, Fujian 350002, China.
| | - Xinying Huang
- Agricultural Product Quality Institute, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, CangShan District, Fuzhou, Fujian 350002, China.
| | - Zhijian Yang
- Agricultural Product Quality Institute, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, CangShan District, Fuzhou, Fujian 350002, China.
| | - Jingui Zheng
- Agricultural Product Quality Institute, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, CangShan District, Fuzhou, Fujian 350002, China.
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Yang Y, Fu D, Zhu C, He Y, Zhang H, Liu T, Li X, Wu C. The RING-Finger Ubiquitin Ligase HAF1 Mediates Heading date 1 Degradation during Photoperiodic Flowering in Rice. THE PLANT CELL 2015; 27:2455-68. [PMID: 26296966 PMCID: PMC4815093 DOI: 10.1105/tpc.15.00320] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/02/2015] [Accepted: 07/31/2015] [Indexed: 05/17/2023]
Abstract
The photoperiodic response is one of the most important factors determining heading date in rice (Oryza sativa). Although rhythmic expression patterns of flowering time genes have been reported to fine-tune the photoperiodic response, posttranslational regulation of key flowering regulators has seldom been elucidated in rice. Heading date 1 (Hd1) encodes a zinc finger transcription factor that plays a crucial role in the photoperiodic response, which determines rice regional adaptability. However, little is known about the molecular mechanisms of Hd1 accumulation during the photoperiod response. Here, we identify a C3HC4 RING domain-containing E3 ubiquitin ligase, Heading date Associated Factor 1 (HAF1), which physically interacts with Hd1. HAF1 mediates ubiquitination and targets Hd1 for degradation via the 26S proteasome-dependent pathway. The haf1 mutant exhibits a later flowering heading date under both short-day and long-day conditions. In addition, the haf1 hd1 double mutant headed as late as hd1 plants under short-day conditions but exhibited a heading date similar to haf1 under long-day conditions, thus indicating that HAF1 may determine heading date mainly through Hd1 under short-day conditions. Moreover, high levels of Hd1 accumulate in haf1. Our results suggest that HAF1 is essential to precise modulation of the timing of Hd1 accumulation during the photoperiod response in rice.
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Affiliation(s)
- Ying Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Chunmei Zhu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yizhou He
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Huijun Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Hou Y, Qiu J, Tong X, Wei X, Nallamilli BR, Wu W, Huang S, Zhang J. A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight. BMC PLANT BIOLOGY 2015; 15:163. [PMID: 26112675 PMCID: PMC4482044 DOI: 10.1186/s12870-015-0541-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/05/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Rice is a major crop worldwide. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has become one of the most devastating diseases for rice. It has been clear that phosphorylation plays essential roles in plant disease resistance. However, the role of phosphorylation is poorly understood in rice-Xoo system. Here, we report the first study on large scale enrichment of phosphopeptides and identification of phosphosites in rice before and 24 h after Xoo infection. RESULTS We have successfully identified 2367 and 2223 phosphosites on 1334 and 1297 representative proteins in 0 h and 24 h after Xoo infection, respectively. A total of 762 differentially phosphorylated proteins, including transcription factors, kinases, epi-genetic controlling factors and many well-known disease resistant proteins, are identified after Xoo infection suggesting that they may be functionally relevant to Xoo resistance. In particular, we found that phosphorylation/dephosphorylation might be a key switch turning on/off many epi-genetic controlling factors, including HDT701, in response to Xoo infection, suggesting that phosphorylation switch overriding the epi-genetic regulation may be a very universal model in the plant disease resistance pathway. CONCLUSIONS The phosphosites identified in this study would be a big complementation to our current knowledge in the phosphorylation status and sites of rice proteins. This research represents a substantial advance in understanding the rice phosphoproteome as well as the mechanism of rice bacterial blight resistance.
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Affiliation(s)
- Yuxuan Hou
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Jiehua Qiu
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Xiaohong Tong
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Xiangjin Wei
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Babi R Nallamilli
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, U.S.A..
| | - Weihuai Wu
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China.
| | - Shiwen Huang
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Jian Zhang
- China National Rice Research Institute, Hangzhou, 311400, China.
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Chen Z, Gao X, Zhang J. Alteration of osa-miR156e expression affects rice plant architecture and strigolactones (SLs) pathway. PLANT CELL REPORTS 2015; 34:767-81. [PMID: 25604991 DOI: 10.1007/s00299-015-1740-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/30/2014] [Accepted: 01/06/2015] [Indexed: 05/20/2023]
Abstract
Overexpressing osa--miR156e in rice produced a bushy mutant and osa--miR156e regulation of tillering may do this through the strigolactones (SLs) pathway. Appropriate downregulation of osa--miR156 expression contributed to the improvement of plant architecture. Tillering is one of the main determinants for rice architecture and yield. In this study, a bushy mutant of rice was identified with increased tiller number, reduced plant height, prolonged heading date, low seed setting, and small panicle size due to a T-DNA insertion which essentially elevated the expression of osa-miR156e. Transgenic plants with constitutive expression of osa-miR156e also had the bushy phenotype, which showed osa-miR156 may control apical dominance and tiller outgrowth via regulating the strigolactones signaling pathway. Furthermore, the extent of impaired morphology was correlated with the expression level of osa-miR156e. In an attempt to genetically improve rice architecture, ectopic expression of osa-miR156e under the GAL4-UAS system or OsTB1 promoter was conducted. According to agronomic trait analysis, pTB1:osa-miR156e transgenic plants significantly improved the grain yield per plant compared to plants overexpressing osa-miR156e, even though the yield was still inferior to the wild type, making it a very interesting albeit negative result. Our results suggested that osa-miR156 could serve as a potential tool for modifying rice plant architecture through genetic manipulation of the osa-miR156 expression level.
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Affiliation(s)
- Zhihui Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China,
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37
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Identification of T-DNA Integration Sites: TAIL-PCR and Sequence Analysis. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10503-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Chen L, Hao L, Parry MAJ, Phillips AL, Hu YG. Progress in TILLING as a tool for functional genomics and improvement of crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:425-43. [PMID: 24618006 DOI: 10.1111/jipb.12192] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/11/2014] [Indexed: 05/18/2023]
Abstract
Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes (TILLING), which combines traditional chemical mutagenesis with high-throughput genome-wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or even allohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small-scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2 (or M3) plants.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Gonçalves GAL, Oliveira PH, Gomes AG, Prather KLJ, Lewis LA, Prazeres DMF, Monteiro GA. Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters. Appl Microbiol Biotechnol 2014; 98:6609-19. [PMID: 24769900 DOI: 10.1007/s00253-014-5695-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 01/29/2023]
Abstract
Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a meta-analysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3' region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability.
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Affiliation(s)
- Geisa A L Gonçalves
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Lisbon, Portugal
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40
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Lu G, Wang X, Liu J, Yu K, Gao Y, Liu H, Wang C, Wang W, Wang G, Liu M, Mao G, Li B, Qin J, Xia M, Zhou J, Liu J, Jiang S, Mo H, Cui J, Nagasawa N, Sivasankar S, Albertsen MC, Sakai H, Mazur BJ, Lassner MW, Broglie RM. Application of T-DNA activation tagging to identify glutamate receptor-like genes that enhance drought tolerance in plants. PLANT CELL REPORTS 2014; 33:617-31. [PMID: 24682459 DOI: 10.1007/s00299-014-1586-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 05/26/2023]
Abstract
A high-quality rice activation tagging population has been developed and screened for drought-tolerant lines using various water stress assays. One drought-tolerant line activated two rice glutamate receptor-like genes. Transgenic overexpression of the rice glutamate receptor-like genes conferred drought tolerance to rice and Arabidopsis. Rice (Oryza sativa) is a multi-billion dollar crop grown in more than one hundred countries, as well as a useful functional genetic tool for trait discovery. We have developed a population of more than 200,000 activation-tagged rice lines for use in forward genetic screens to identify genes that improve drought tolerance and other traits that improve yield and agronomic productivity. The population has an expected coverage of more than 90 % of rice genes. About 80 % of the lines have a single T-DNA insertion locus and this molecular feature simplifies gene identification. One of the lines identified in our screens, AH01486, exhibits improved drought tolerance. The AH01486 T-DNA locus is located in a region with two glutamate receptor-like genes. Constitutive overexpression of either glutamate receptor-like gene significantly enhances the drought tolerance of rice and Arabidopsis, thus revealing a novel function of this important gene family in plant biology.
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Affiliation(s)
- Guihua Lu
- Beijing Kaituo DNA Biotech Research Center, Co., Ltd., Beijing, 102206, China,
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Analysis of T-DNA/Host-Plant DNA Junction Sequences in Single-Copy Transgenic Barley Lines. BIOLOGY 2014; 3:39-55. [PMID: 24833334 PMCID: PMC4009757 DOI: 10.3390/biology3010039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/03/2014] [Accepted: 01/03/2014] [Indexed: 01/19/2023]
Abstract
Sequencing across the junction between an integrated transfer DNA (T-DNA) and a host plant genome provides two important pieces of information. The junctions themselves provide information regarding the proportion of T-DNA which has integrated into the host plant genome, whilst the transgene flanking sequences can be used to study the local genetic environment of the integrated transgene. In addition, this information is important in the safety assessment of GM crops and essential for GM traceability. In this study, a detailed analysis was carried out on the right-border T-DNA junction sequences of single-copy independent transgenic barley lines. T-DNA truncations at the right-border were found to be relatively common and affected 33.3% of the lines. In addition, 14.3% of lines had rearranged construct sequence after the right border break-point. An in depth analysis of the host-plant flanking sequences revealed that a significant proportion of the T-DNAs integrated into or close to known repetitive elements. However, this integration into repetitive DNA did not have a negative effect on transgene expression.
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Wei FJ, Droc G, Guiderdoni E, Hsing YIC. International Consortium of Rice Mutagenesis: resources and beyond. RICE (NEW YORK, N.Y.) 2013; 6:39. [PMID: 24341871 PMCID: PMC3946042 DOI: 10.1186/1939-8433-6-39] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/04/2013] [Indexed: 05/20/2023]
Abstract
Rice is one of the most important crops in the world. The rice community needs to cooperate and share efforts and resources so that we can understand the functions of rice genes, especially those with a role in important agronomical traits, for application in agricultural production. Mutation is a major source of genetic variation that can be used for studying gene function. We will present here the status of mutant collections affected in a random manner by physical/chemical and insertion mutageneses.As of early September 2013, a total of 447, 919 flanking sequence tags from rice mutant libraries with T-DNA, Ac/Ds, En/Spm, Tos17, nDART/aDART insertions have been collected and publicly available. From these, 336,262 sequences are precisely positioned on the japonica rice chromosomes, and 67.5% are in gene interval. We discuss the genome coverage and preference of the insertion, issues limiting the exchange and use of the current collections, as well as new and improved resources. We propose a call to renew all mutant populations as soon as possible. We also suggest that a common web portal should be established for ordering seeds.
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Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Hsing: Rm312, IPMB, Academia Sinica, Nankang District, Taipei 11529 Taiwan
| | - Gaëtan Droc
- CIRAD, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Cirad - av. Agropolis -TA A-108/03, 34398 Montpellier Cedex 5, France
| | - Emmanuel Guiderdoni
- CIRAD, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Cirad - av. Agropolis -TA A-108/03, 34398 Montpellier Cedex 5, France
| | - Yue-ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Hsing: Rm312, IPMB, Academia Sinica, Nankang District, Taipei 11529 Taiwan
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Long T, Guo D, He D, Shen W, Li X. The tRNA 3'-end processing enzyme tRNase Z2 contributes to chloroplast biogenesis in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:1104-18. [PMID: 24034348 DOI: 10.1111/jipb.12102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/19/2013] [Indexed: 05/08/2023]
Abstract
tRNase Z (TRZ) is a ubiquitous endonuclease that removes the 3'-trailer from precursor tRNAs during maturation. In yeast and animals, TRZ regulates the cell cycle via its (t)RNA processing activity; however, its physiological function in higher plants has not been well characterized. This study describes the identification of a rice (Oryza sativa) TRZ2 mutant; plants homozygous for the osatrz2 mutation were albinos with deficient chlorophyll content. A microscopic analysis of the mutant plants revealed that the transition of proplastids to chloroplasts was arrested at an early stage, and the number and size of the plastids in callus cells was substantially decreased. A genetic complementation test and an RNA interference analysis confirmed that disruption of OsaTRZ2 was responsible for the mutant phenotype. OsaTRZ2 is expressed in all rice tissues, but is preferentially expressed in leaves, sheathes, and calli. OsaTRZ2 was subcellularly localized in chloroplasts, and displayed tRNA 3'-end processing activity in both in vitro and in vivo assays. In the osatrz2 mutants, transcription of plastid-encoded and nucleus-encoded RNA polymerases was severely reduced and moderately increased, respectively. These results suggest that the tRNA 3' processing activity of OsaTRZ2 contributes to chloroplast biogenesis.
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Affiliation(s)
- Tuan Long
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Yang Y, Li Y, Wu C. Genomic resources for functional analyses of the rice genome. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:157-63. [PMID: 23571012 DOI: 10.1016/j.pbi.2013.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 03/15/2013] [Accepted: 03/15/2013] [Indexed: 05/07/2023]
Abstract
With the availability of the rice genome sequence, rice research communities are entering a new era of plant functional genomics. The last decade has seen rapid worldwide progress on establishing platforms for rice functional genomic research. These platforms offer practical toolkits and genomic resources for high-throughput identification of genes and pathways. In this review, we summarize available genomic resources for functional analyses of the rice genome. These genomic resources include high-quality bacterial artificial chromosome libraries, large-scale expression sequence tags, full-length cDNA collections, large amounts of data on global expression profiles, various mutant libraries and integrated bioinformatics databases. We not only present the current status of genomic resources but also discuss their usage in elucidating gene functions of the rice genome.
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Affiliation(s)
- Ying Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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Wang N, Long T, Yao W, Xiong L, Zhang Q, Wu C. Mutant resources for the functional analysis of the rice genome. MOLECULAR PLANT 2013; 6:596-604. [PMID: 23204502 DOI: 10.1093/mp/sss142] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large number of rice mutant lines, including those created by T-DNA insertion, Ds/dSpm tagging, Tos17 tagging, and chemical/irradiation mutagenesis, have been generated by groups around the world. In this study, we have reviewed the current status of mutant resources for functional analysis of the rice genome. A total of 246 566 flanking sequence tags from rice mutant libraries with T-DNA, Ds/dSpm, or Tos17 insertion have been collected and analyzed. The results show that, among 211 470 unique hits, inserts located in the genic region account for 68.16%, and 60.49% of nuclear genes contain at least one insertion. Currently, 57% of non-transposable-element-related genes in rice have insertional tags. In addition, chemical/irradiation-induced rice mutant libraries have contributed a lot to both gene identification and new technology for the identification of mutant sites. In this review, we summarize how these tools have been used to generate a large collection of mutants. In addition, we discuss the merits of classic mutation strategies. In order to achieve saturation of mutagenesis in rice, DNA targeting, and new resources like RiceFox for gene functional identification are reviewed from a perspective of the future generation of rice mutant resources.
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Affiliation(s)
- Nili Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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Resequencing rice genomes: an emerging new era of rice genomics. Trends Genet 2013; 29:225-32. [DOI: 10.1016/j.tig.2012.12.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/27/2012] [Accepted: 12/07/2012] [Indexed: 11/19/2022]
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Yang Y, Peng Q, Chen GX, Li XH, Wu CY. OsELF3 is involved in circadian clock regulation for promoting flowering under long-day conditions in rice. MOLECULAR PLANT 2013; 6:202-15. [PMID: 22888152 DOI: 10.1093/mp/sss062] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Heading date is a critical trait that determines cropping seasons and regional adaptability in rice (Oryza sativa). Research efforts during the last decade have identified some important photoperiod pathway genes that are conserved between Arabidopsis and rice. In this study, we identified a novel gene, Oryza sativa ELF3 (OsELF3), which is a putative homolog of the ELF3 gene in Arabidopsis thaliana. OsELF3 was required for the control of heading date under long-day conditions. Its Tos17-tagging mutants exhibited a delayed heading date phenotype only under long-day, but not short-day, conditions. OsELF3 was highly expressed in leaf blades, and the OsELF3 protein was localized in the nucleolus. An obvious diurnal rhythm of OsELF3 transcript level was observed, with a trough in the early day and a peak in the late night in wild-type plants. However, this expression pattern was disrupted in oself3 mutants. Further investigations showed that the expression of OsGI and Ghd7 was up-regulated in the oself3 mutant, indicating that OsELF3 acts as a negative regulator upstream of OsGI and Ghd7 in the flowering-time control under long-day conditions. The rhythmic expression of circadian clock-related genes, including some OsPRR members, was obviously affected in oself3 mutants. Our results indicated that OsELF3 acts as a floral activator in the long-day photoperiodic pathway via its crosstalk with the circadian clock in rice.
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Affiliation(s)
- Ying Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research-Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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Chang Y, Long T, Wu C. Effort and contribution of T-DNA Insertion mutant library for rice functional genomics research in China: review and perspective. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:953-966. [PMID: 23020748 DOI: 10.1111/j.1744-7909.2012.01171.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
With the completion of the rice (Oryza sativa L.) genome-sequencing project, the rice research community proposed to characterize the function of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.
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Affiliation(s)
- Yuxiao Chang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research-Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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Bragg JN, Wu J, Gordon SP, Guttman ME, Thilmony R, Lazo GR, Gu YQ, Vogel JP. Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLoS One 2012; 7:e41916. [PMID: 23028431 PMCID: PMC3444500 DOI: 10.1371/journal.pone.0041916] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/29/2012] [Indexed: 11/18/2022] Open
Abstract
The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optimized our Agrobacterium tumefaciens-mediated high-efficiency transformation method and generated 8,491 Brachypodium T-DNA lines. We used inverse PCR to sequence the DNA flanking the insertion sites in the mutants. Using these flanking sequence tags (FSTs) we were able to assign 7,389 FSTs from 4,402 T-DNA mutants to 5,285 specific insertion sites (ISs) in the Brachypodium genome. More than 29% of the assigned ISs are supported by multiple FSTs. T-DNA insertions span the entire genome with an average of 19.3 insertions/Mb. The distribution of T-DNA insertions is non-uniform with a larger number of insertions at the distal ends compared to the centromeric regions of the chromosomes. Insertions are correlated with genic regions, but are biased toward UTRs and non-coding regions within 1 kb of genes over exons and intron regions. More than 1,300 unique genes have been tagged in this population. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest.
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Affiliation(s)
- Jennifer N. Bragg
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- University of California Davis, Davis, California, United States of America
| | - Jiajie Wu
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- University of California Davis, Davis, California, United States of America
| | - Sean P. Gordon
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Mara E. Guttman
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Roger Thilmony
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Gerard R. Lazo
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Yong Q. Gu
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- * E-mail:
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Incidence of genome structure, DNA asymmetry, and cell physiology on T-DNA integration in chromosomes of the phytopathogenic fungus Leptosphaeria maculans. G3-GENES GENOMES GENETICS 2012; 2:891-904. [PMID: 22908038 PMCID: PMC3411245 DOI: 10.1534/g3.112.002048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 06/07/2012] [Indexed: 11/18/2022]
Abstract
The ever-increasing generation of sequence data is accompanied by unsatisfactory functional annotation, and complex genomes, such as those of plants and filamentous fungi, show a large number of genes with no predicted or known function. For functional annotation of unknown or hypothetical genes, the production of collections of mutants using Agrobacterium tumefaciens–mediated transformation (ATMT) associated with genotyping and phenotyping has gained wide acceptance. ATMT is also widely used to identify pathogenicity determinants in pathogenic fungi. A systematic analysis of T-DNA borders was performed in an ATMT-mutagenized collection of the phytopathogenic fungus Leptosphaeria maculans to evaluate the features of T-DNA integration in its particular transposable element-rich compartmentalized genome. A total of 318 T-DNA tags were recovered and analyzed for biases in chromosome and genic compartments, existence of CG/AT skews at the insertion site, and occurrence of microhomologies between the T-DNA left border (LB) and the target sequence. Functional annotation of targeted genes was done using the Gene Ontology annotation. The T-DNA integration mainly targeted gene-rich, transcriptionally active regions, and it favored biological processes consistent with the physiological status of a germinating spore. T-DNA integration was strongly biased toward regulatory regions, and mainly promoters. Consistent with the T-DNA intranuclear-targeting model, the density of T-DNA insertion correlated with CG skew near the transcription initiation site. The existence of microhomologies between promoter sequences and the T-DNA LB flanking sequence was also consistent with T-DNA integration to host DNA mediated by homologous recombination based on the microhomology-mediated end-joining pathway.
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