1
|
Nguyen DT, Zavadil Kokáš F, Gonin M, Lavarenne J, Colin M, Gantet P, Bergougnoux V. Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.). BMC PLANT BIOLOGY 2024; 24:438. [PMID: 38778283 PMCID: PMC11110440 DOI: 10.1186/s12870-024-05160-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering. RESULTS Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process. CONCLUSIONS This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.
Collapse
Affiliation(s)
- Dieu Thu Nguyen
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- Department of Biochemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Filip Zavadil Kokáš
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- Present address: Masaryk Memorial Cancer Institute, Brno, Czechia
| | - Mathieu Gonin
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jérémy Lavarenne
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Myriam Colin
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Pascal Gantet
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia.
| |
Collapse
|
2
|
Muzaffar A, Chen Y, Lee H, Wu C, Le TT, Liang J, Lu C, Balasubramaniam H, Lo S, Yu L, Chan C, Chen K, Lee M, Hsing Y, Ho TD, Yu S. A newly evolved rice-specific gene JAUP1 regulates jasmonate biosynthesis and signalling to promote root development and multi-stress tolerance. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1417-1432. [PMID: 38193234 PMCID: PMC11022792 DOI: 10.1111/pbi.14276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 12/01/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024]
Abstract
Root architecture and function are critical for plants to secure water and nutrient supply from the soil, but environmental stresses alter root development. The phytohormone jasmonic acid (JA) regulates plant growth and responses to wounding and other stresses, but its role in root development for adaptation to environmental challenges had not been well investigated. We discovered a novel JA Upregulated Protein 1 gene (JAUP1) that has recently evolved in rice and is specific to modern rice accessions. JAUP1 regulates a self-perpetuating feed-forward loop to activate the expression of genes involved in JA biosynthesis and signalling that confers tolerance to abiotic stresses and regulates auxin-dependent root development. Ectopic expression of JAUP1 alleviates abscisic acid- and salt-mediated suppression of lateral root (LR) growth. JAUP1 is primarily expressed in the root cap and epidermal cells (EPCs) that protect the meristematic stem cells and emerging LRs. Wound-activated JA/JAUP1 signalling promotes crosstalk between the root cap of LR and parental root EPCs, as well as induces cell wall remodelling in EPCs overlaying the emerging LR, thereby facilitating LR emergence even under ABA-suppressive conditions. Elevated expression of JAUP1 in transgenic rice or natural rice accessions enhances abiotic stress tolerance and reduces grain yield loss under a limited water supply. We reveal a hitherto unappreciated role for wound-induced JA in LR development under abiotic stress and suggest that JAUP1 can be used in biotechnology and as a molecular marker for breeding rice adapted to extreme environmental challenges and for the conservation of water resources.
Collapse
Affiliation(s)
- Adnan Muzaffar
- Molecular and Cell Biology, Taiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Life SciencesNational Defense Medical CenterTaipeiTaiwan, ROC
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Yi‐Shih Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Hsiang‐Ting Lee
- Molecular and Cell Biology, Taiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Life SciencesNational Defense Medical CenterTaipeiTaiwan, ROC
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Cheng‐Chieh Wu
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Trang Thi Le
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Jin‐Zhang Liang
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Department of Agricultural ChemistryNational Taiwan UniversityTaipeiTaiwan, ROC
| | - Chun‐Hsien Lu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Genome and Systems Biology Degree ProgramNational Taiwan University and Academia SinicaTaipeiTaiwan, ROC
| | - Hariharan Balasubramaniam
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate ProgramAcademia Sinica and National Chung Hsing UniversityTaipeiTaiwan, ROC
| | - Shuen‐Fang Lo
- International Bachelor Program of AgribusinessNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Lin‐Chih Yu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Chien‐Hao Chan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Ku‐Ting Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Miin‐Huey Lee
- Department of Plant PathologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Yue‐Ie Hsing
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Tuan‐Hua David Ho
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Su‐May Yu
- Molecular and Cell Biology, Taiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Life SciencesNational Defense Medical CenterTaipeiTaiwan, ROC
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Genome and Systems Biology Degree ProgramNational Taiwan University and Academia SinicaTaipeiTaiwan, ROC
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate ProgramAcademia Sinica and National Chung Hsing UniversityTaipeiTaiwan, ROC
- Department of Plant PathologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| |
Collapse
|
3
|
Gandikota M, Krishnakanth Yadav T, Maram RR, Kalluru S, Sena MB, Siddiq EA, Kalinati Narasimhan Y, Vemireddy LR, Ghanta A. Development of activation-tagged gain-of-functional mutants in indica rice line (BPT 5204) for sheath blight resistance. Mol Biol Rep 2024; 51:381. [PMID: 38430361 DOI: 10.1007/s11033-023-09194-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/21/2023] [Indexed: 03/03/2024]
Abstract
BACKGROUND The development of sheath blight (ShB) resistance varieties has been a challenge for scientists for long time in rice. Activation tagging is an efficient gain-of-function mutation approach to create novel phenotypes and to identify their underlying genes. In this study, a mutant population was developed employing activation tagging in the recalcitrant indica rice (Oryza sativa L.) cv. BPT 5204 (Samba Mahsuri) through activation tagging. METHODS AND RESULTS In this study, we have generated more than 1000 activation tagged lines in indica rice, from these mutant population 38 (GFP- RFP+) stable Ds plants were generated through germinal transposition at T2 generation based on molecular analysis and seeds selected on hygromycin (50 mg/L) containing medium segregation analyses confirmed that the transgene inherited as mendelian segregation ratio of 3:1 (3 resistant: 1 susceptible). Of them, five stable activation tagged Ds lines (M-Ds-1, M-Ds-2, M-Ds-3, M-Ds-4 and M-Ds-5) were selected based on phenotypic observation through screening for sheath blight (ShB) resistance caused by fungal pathogen Rhizoctonia solani (R. solani),. Among them, M-Ds-3 and M-Ds-5 lines showed significant resistance for ShB over other tagged lines and wild type (WT) plants. Furthermore, analysed for launch pad insertion through TAIL-PCR results and mapped on corresponding rice chromosomes. Flanking sequence and gene expression analysis revealed that the upregulation of glycoside hydrolase-OsGH or similar to Class III chitinase homologue (LOC_Os08g40680) in M-Ds-3 and a hypothetical protein gene (LOC_Os01g55000) in M-Ds-5 are potential candidate genes for sheath blight resistance in rice. CONCLUSION In the present study, we developed Ac-Ds based ShB resistance gain-of-functional mutants through activation tagging in rice. These activation tagged mutant lines can be excellent sources for the development of ShB resistant cultivars in rice.
Collapse
Affiliation(s)
- Mahendranath Gandikota
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - T Krishnakanth Yadav
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | | | - Sudhamani Kalluru
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya N.G. Ranaga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - M Balachandran Sena
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - E A Siddiq
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | - Yamini Kalinati Narasimhan
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya N.G. Ranaga Agricultural University (ANGRAU), Tirupati, 517502, India.
| | - Anuradha Ghanta
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India.
| |
Collapse
|
4
|
Raj SRG, Nadarajah K. QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals. Int J Mol Sci 2022; 24:ijms24010006. [PMID: 36613450 PMCID: PMC9820233 DOI: 10.3390/ijms24010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.
Collapse
|
5
|
Lo SF, Chatterjee J, Biswal AK, Liu IL, Chang YP, Chen PJ, Wanchana S, Elmido-Mabilangan A, Nepomuceno RA, Bandyopadhyay A, Hsing YI, Quick WP. Closer vein spacing by ectopic expression of nucleotide-binding and leucine-rich repeat proteins in rice leaves. PLANT CELL REPORTS 2022; 41:319-335. [PMID: 34837515 PMCID: PMC8850240 DOI: 10.1007/s00299-021-02810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Elevated expression of nucleotide-binding and leucine-rich repeat proteins led to closer vein spacing and higher vein density in rice leaves. To feed the growing global population and mitigate the negative effects of climate change, there is a need to improve the photosynthetic capacity and efficiency of major crops such as rice to enhance grain yield potential. Alterations in internal leaf morphology and cellular architecture are needed to underpin some of these improvements. One of the targets is to generate a "Kranz-like" anatomy in leaves that includes decreased interveinal spacing close to that in C4 plant species. As C4 photosynthesis has evolved from C3 photosynthesis independently in multiple lineages, the genes required to facilitate C4 may already be present in the rice genome. The Taiwan Rice Insertional Mutants (TRIM) population offers the advantage of gain-of-function phenotype trapping, which accelerates the identification of rice gene function. In the present study, we screened the TRIM population to determine the extent to which genetic plasticity can alter vein density (VD) in rice. Close vein spacing mutant 1 (CVS1), identified from a VD screening of approximately 17,000 TRIM lines, conferred heritable high leaf VD. Increased vein number in CVS1 was confirmed to be associated with activated expression of two nucleotide-binding and leucine-rich repeat (NB-LRR) proteins. Overexpression of the two NB-LRR genes individually in rice recapitulates the high VD phenotype, due mainly to reduced interveinal mesophyll cell (M cell) number, length, bulliform cell size and thus interveinal distance. Our studies demonstrate that the trait of high VD in rice can be achieved by elevated expression of NB-LRR proteins limited to no yield penalty.
Collapse
Affiliation(s)
- Shuen-Fang Lo
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC.
| | - Jolly Chatterjee
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Akshaya K Biswal
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz km. 45, El Batán, Texcoco, CP 56237, México
| | - I-Lun Liu
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Yu-Pei Chang
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Pei-Jing Chen
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Samart Wanchana
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | | | - Robert A Nepomuceno
- National Institute of Molecular Biology and Biotechnology, University of the Philippines (BIOTECH-UPLB), Los Baños, 4031, Philippines
| | | | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - William Paul Quick
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines.
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
| |
Collapse
|
6
|
Zhou X, Shafique K, Sajid M, Ali Q, Khalili E, Javed MA, Haider MS, Zhou G, Zhu G. Era-like GTP protein gene expression in rice. BRAZ J BIOL 2021; 82:e250700. [PMID: 34259718 DOI: 10.1590/1519-6984.250700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/19/2021] [Indexed: 11/22/2022] Open
Abstract
The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.
Collapse
Affiliation(s)
- X Zhou
- Linyi University, College of Life Science, Linyi, Shandong, China
| | - K Shafique
- Government Sadiq College Women University, Department of Botany, Bahawalpur, Pakistan
| | - M Sajid
- University of Okara, Faculty of Life Sciences, Department of Biotechnology, Okara, Pakistan
| | - Q Ali
- University of Lahore, Institute of Molecular Biology and Biotechnology, Lahore, Pakistan
| | - E Khalili
- Tarbiat Modarres University, Faculty of Science, Department of Plant Science, Tehran, Iran
| | - M A Javed
- University of the Punjab Lahore, Department of Plant Breeding and Genetics, Lahore, Pakistan
| | - M S Haider
- University of the Punjab Lahore, Department of Plant Pathology, Lahore, Pakistan
| | - G Zhou
- Yangzhou University, The Ministry of Education of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, Jiangsu, China
| | - G Zhu
- Yangzhou University, The Ministry of Education of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, Jiangsu, China
| |
Collapse
|
7
|
Lo S, Cheng M, Hsing YC, Chen Y, Lee K, Hong Y, Hsiao Y, Hsiao A, Chen P, Wong L, Chen N, Reuzeau C, Ho TD, Yu S. Rice Big Grain 1 promotes cell division to enhance organ development, stress tolerance and grain yield. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1969-1983. [PMID: 32034845 PMCID: PMC7415788 DOI: 10.1111/pbi.13357] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 01/07/2020] [Accepted: 01/19/2020] [Indexed: 05/18/2023]
Abstract
Grain/seed yield and plant stress tolerance are two major traits that determine the yield potential of many crops. In cereals, grain size is one of the key factors affecting grain yield. Here, we identify and characterize a newly discovered gene Rice Big Grain 1 (RBG1) that regulates grain and organ development, as well as abiotic stress tolerance. Ectopic expression of RBG1 leads to significant increases in the size of not only grains but also other major organs such as roots, shoots and panicles. Increased grain size is primarily due to elevated cell numbers rather than cell enlargement. RBG1 is preferentially expressed in meristematic and proliferating tissues. Ectopic expression of RBG1 promotes cell division, and RBG1 co-localizes with microtubules known to be involved in cell division, which may account for the increase in organ size. Ectopic expression of RBG1 also increases auxin accumulation and sensitivity, which facilitates root development, particularly crown roots. Moreover, overexpression of RBG1 up-regulated a large number of heat-shock proteins, leading to enhanced tolerance to heat, osmotic and salt stresses, as well as rapid recovery from water-deficit stress. Ectopic expression of RBG1 regulated by a specific constitutive promoter, GOS2, enhanced harvest index and grain yield in rice. Taken together, we have discovered that RBG1 regulates two distinct and important traits in rice, namely grain yield and stress tolerance, via its effects on cell division, auxin and stress protein induction.
Collapse
Affiliation(s)
- Shuen‐Fang Lo
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Ming‐Lung Cheng
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
| | | | - Yi‐Shih Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Kuo‐Wei Lee
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Ya‐Fang Hong
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Yu Hsiao
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - An‐Shan Hsiao
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Pei‐Jing Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Lai‐In Wong
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Nan‐Chen Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | | | - Tuan‐Hua David Ho
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Department of Life SciencesNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Su‐May Yu
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
- Department of Life SciencesNational Chung Hsing UniversityTaichungTaiwan, ROC
| |
Collapse
|
8
|
Sánchez-Sanuy F, Peris-Peris C, Tomiyama S, Okada K, Hsing YI, San Segundo B, Campo S. Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus. BMC PLANT BIOLOGY 2019; 19:563. [PMID: 31852430 PMCID: PMC6921540 DOI: 10.1186/s12870-019-2156-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 11/21/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in eukaryotes. In rice, MIR7695 expression is regulated by infection with the rice blast fungus Magnaporthe oryzae with subsequent down-regulation of an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6). NRAMP6 functions as an iron transporter in rice. RESULTS Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance. During pathogen infection, iron accumulated in the vicinity of M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced iron accumulation and resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCPS4, were also highly upregulated in wild-type rice plants grown under high iron supply. CONCLUSIONS Our data support a positive role of miR7695 in regulating rice immunity that further underpin links between defense and iron signaling in rice. These findings provides a basis to better understand regulatory mechanisms involved in rice immunity in which miR7695 participates which has a great potential for the development of strategies to improve blast resistance in rice.
Collapse
Affiliation(s)
- Ferran Sánchez-Sanuy
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Cristina Peris-Peris
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Shiho Tomiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yue-Ie Hsing
- Institute of Plant and Microrbial Biology, Academia Sinica, Taipei, Taiwan
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| |
Collapse
|
9
|
Frank U, Kublik S, Mayer D, Engel M, Schloter M, Durner J, Gaupels F. A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing. BMC PLANT BIOLOGY 2019; 19:539. [PMID: 31801481 PMCID: PMC6894221 DOI: 10.1186/s12870-019-2162-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Nitrogen dioxide (NO2) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death. RESULTS Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO2 fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO2 whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO2. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO2-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation. CONCLUSIONS The presented NO2 dead-or-alive screen combined with next-generation sequencing after T-DNA-specific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.
Collapse
Affiliation(s)
- Ulrike Frank
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dörte Mayer
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marion Engel
- Scientific Computing Research Unit, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, Freising, Germany
| | - Frank Gaupels
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
| |
Collapse
|
10
|
Viana VE, Pegoraro C, Busanello C, Costa de Oliveira A. Mutagenesis in Rice: The Basis for Breeding a New Super Plant. FRONTIERS IN PLANT SCIENCE 2019; 10:1326. [PMID: 31781133 PMCID: PMC6857675 DOI: 10.3389/fpls.2019.01326] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.
Collapse
Affiliation(s)
| | | | | | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Rio Grande do Sul, Brazil
| |
Collapse
|
11
|
Singh B, Salaria N, Thakur K, Kukreja S, Gautam S, Goutam U. Functional genomic approaches to improve crop plant heat stress tolerance. F1000Res 2019; 8:1721. [PMID: 31824669 PMCID: PMC6896246 DOI: 10.12688/f1000research.19840.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
Heat stress as a yield limiting issue has become a major threat for food security as global warming progresses. Being sessile, plants cannot avoid heat stress. They respond to heat stress by activating complex molecular networks, such as signal transduction, metabolite production and expressions of heat stress-associated genes. Some plants have developed an intricate signalling network to respond and adapt it. Heat stress tolerance is a polygenic trait, which is regulated by various genes, transcriptional factors, proteins and hormones. Therefore, to improve heat stress tolerance, a sound knowledge of various mechanisms involved in the response to heat stress is required. The classical breeding methods employed to enhance heat stress tolerance has had limited success. In this era of genomics, next generation sequencing techniques, availability of genome sequences and advanced biotechnological tools open several windows of opportunities to improve heat stress tolerance in crop plants. This review discusses the potential of various functional genomic approaches, such as genome wide association studies, microarray, and suppression subtractive hybridization, in the process of discovering novel genes related to heat stress, and their functional validation using both reverse and forward genetic approaches. This review also discusses how these functionally validated genes can be used to improve heat stress tolerance through plant breeding, transgenics and genome editing approaches.
Collapse
Affiliation(s)
- Baljeet Singh
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Neha Salaria
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Kajal Thakur
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Sarvjeet Kukreja
- School of Agriculture, Lovely Professional University, Phagwara, Jalandhar, 144411, India
| | - Shristy Gautam
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Umesh Goutam
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| |
Collapse
|
12
|
Liao CC, Chen LJ, Lo SF, Chen CW, Chu YW. EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches. PLoS Comput Biol 2019; 15:e1006942. [PMID: 31067213 PMCID: PMC6505892 DOI: 10.1371/journal.pcbi.1006942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/09/2019] [Indexed: 11/17/2022] Open
Abstract
T-DNA activation-tagging technology is widely used to study rice gene functions. When T-DNA inserts into genome, the flanking gene expression may be altered using CaMV 35S enhancer, but the affected genes still need to be validated by biological experiment. We have developed the EAT-Rice platform to predict the flanking gene expression of T-DNA insertion site in rice mutants. The three kinds of DNA sequences including UPS1K, DISTANCE, and MIDDLE were retrieved to encode and build a forecast model of two-layer machine learning. In the first-layer models, the features nucleotide context (N-gram), cis-regulatory elements (Motif), nucleotide physicochemical properties (NPC), and CG-island (CGI) were used to build SVM models by analysing the concealed information embedded within the three kinds of sequences. Logistic regression was used to estimate the probability of gene activation which as feature-encoding weighting within first-layer model. In the second-layer models, the NaiveBayesUpdateable algorithm was used to integrate these first layer-models, and the system performance was 88.33% on 5-fold cross-validation, and 79.17% on independent-testing finally. In the three kinds of sequences, the model constructed by Middle had the best contribution to the system for identifying the activated genes. The EAT-Rice system provided better performance and gene expression prediction at further distances when compared to the TRIM database. An online server based on EAT-rice is available at http://predictor.nchu.edu.tw/EAT-Rice.
Collapse
Affiliation(s)
- Chi-Chou Liao
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Advanced Plant Biotechnology Center National Chung Hsing University, Taichung, Taiwan
| | - Shuen-Fang Lo
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Wei Chen
- Department of Computer Science and Engineering, National Chung Hsing University, Taichung, Taiwan
| | - Yen-Wei Chu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.,Rong Hsing Research Center For Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| |
Collapse
|
13
|
Mutation Breeding of a N-methyl-N-nitrosourea (MNU)-Induced Rice (Oryza sativa L. ssp. Indica) Population for the Yield Attributing Traits. SUSTAINABILITY 2019. [DOI: 10.3390/su11041062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Difficulties in breeding new rice cultivars that have a high yield, are acceptable quality, and are tolerant to environmental stresses have been the major constraint of rice production in many developing countries, as these traits are determined by multiple genes associated with complicated and uncontrollable gene segregations.Furthermore, the gene/QTL (quantitative trait locus) introduced to the cultivar is unstable due to the interaction among the active genes, which determine the phenotypic performance, not yet been well understood or controllable. In this study, the N-methyl-N-nitrosourea (MNU)-induced mutation was applied to the heterozygote of the F1 generation from the cross between TBR1 (female) and KD18 (male parent). The phenotype and genotype of the M2 and M3 generations were evaluated and showed that the mutant population phenotypes, including the plant height, semi-dwarfism, amylose content, protein content, gel consistency, grain yield, and spikelet fertility, varied. Interestingly, no segregation among the genotypes in the M2 and M3 generations was observed, while the genotypes of the control population were either paternally inherited or indeterminable when using 28 polymorphism simple sequence repeat (SSR) markers that were identified on parental lines from 200 markers. The MNU-induced mutation caused maternal inheritance in the segregating populations, as primarily important agronomic traits were maternally succeeded from the female line TBR1. The findings of this study indicated that, through the use of MNU, the breeding of rice cultivars with close genetic backgrounds (similarity coefficient = 0.52) could be shortened by the maternal control of important qualities, such as pest and disease resistance and high yield, thus contributing to sustainable rice production for rice farmers. Further examination of rice cultivars with a greater difference in the genetic background should be subsequently conducted.
Collapse
|
14
|
Anh TTT, Xuan TD, Huong CT, Dat TD. Phenotypic Performance of Rice ( Oryza sativa L .) Populations Induced by the MNU Mutant on the Adaptive Characteristics. ACTA ACUST UNITED AC 2019. [DOI: 10.18052/www.scipress.com/jhpr.5.13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mutation is an impressive method to induce potent characteristics in rice breeding. Evaluation on the phenotypic perfomance in mutant populations is important to examine the effectiveness of mutation. In this study, two rice populations of MNU ((N-methyl-N-Nitrosourea) -induced mutants were used to evaluate their phenotypes. The results showed that all of varieties and mutants expressed their ability to adapt with new environment condition via phenotypic expression. Grain yield of them ranged from 6.18 to 10.70 tons/ha. In general population S/TB performed their best characters. The distribution of related traits to grain yield and amylose content were also different from each population. It was observed that mutants expressed better characters than their parents. This study provided general information on phenotype of rice mutants and varieties in new environmental condition and revealed better adaptive characteristics of rice mutants. Findings of this study confirmed the the efficacy of MNU in rice breeding.
Collapse
|
15
|
Wu HP, Wei FJ, Wu CC, Lo SF, Chen LJ, Fan MJ, Chen S, Wen IC, Yu SM, Ho THD, Lai MH, Hsing YIC. Large-scale phenomics analysis of a T-DNA tagged mutant population. Gigascience 2018; 6:1-7. [PMID: 28854617 PMCID: PMC5570018 DOI: 10.1093/gigascience/gix055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/04/2017] [Indexed: 01/26/2023] Open
Abstract
Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons.
Collapse
Affiliation(s)
- Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Institute of Plant Biology, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Ming-Jen Fan
- Department of Biotechnology, Asia University, 500, Lioufeng Road, Taichung 413, Taiwan
| | - Shu Chen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Ien-Chie Wen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Department of Agronomy, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| |
Collapse
|
16
|
Sharma M, Pandey GK. Editorial: Genomics and Functional Genomics of Stress-mediated Signaling in Plants: Volume II. Curr Genomics 2018; 19:2-3. [PMID: 29491727 PMCID: PMC5817873 DOI: 10.2174/138920291901171201141313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
17
|
Petit J, Bres C, Mauxion JP, Bakan B, Rothan C. Breeding for cuticle-associated traits in crop species: traits, targets, and strategies. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5369-5387. [PMID: 29036305 DOI: 10.1093/jxb/erx341] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/14/2017] [Indexed: 05/18/2023]
Abstract
Improving crop productivity and quality while promoting sustainable agriculture have become major goals in plant breeding. The cuticle is a natural film covering the aerial organs of plants and consists of lipid polyesters covered and embedded with wax. The cuticle protects plants against water loss and pathogens and affects traits with strong impacts on crop quality such as, for horticultural crops, fruit brightness, cracking, russeting, netting, and shelf life. Here we provide an overview of the most important cuticle-associated traits that can be targeted for crop improvement. To date, most studies on cuticle-associated traits aimed at crop breeding have been done on fleshy fruits. Less information is available for staple crops such as rice, wheat or maize. Here we present new insights into cuticle formation and properties resulting from the study of genetic resources available for the various crop species. Our review also covers the current strategies and tools aimed at exploiting available natural and artificially induced genetic diversity and the technologies used to transfer the beneficial alleles affecting cuticle-associated traits to commercial varieties.
Collapse
Affiliation(s)
- Johann Petit
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
| | - Cécile Bres
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
| | | | | | - Christophe Rothan
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
| |
Collapse
|
18
|
Cheng ML, Lo SF, Hsiao AS, Hong YF, Yu SM, Ho THD. Ectopic Expression of WINDING 1 Leads to Asymmetrical Distribution of Auxin and a Spiral Phenotype in Rice. PLANT & CELL PHYSIOLOGY 2017; 58:1494-1506. [PMID: 28922746 DOI: 10.1093/pcp/pcx088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Ectopic expression of the rice WINDING 1 (WIN1) gene leads to a spiral phenotype only in shoots but not in roots. Rice WIN1 belongs to a specific class of proteins in cereal plants containing a Bric-a-Brac/Tramtrack/Broad (BTB) complex, a non-phototropic hypocotyl 3 (NPH3) domain and a coiled-coil motif. The WIN1 protein is predominantly localized to the plasma membrane, but is also co-localized to plasmodesmata, where it exhibits a punctate pattern. It is observed that WIN1 is normally expressed in roots and the shoot-root junction, but not in the rest of shoots. In roots, WIN1 is largely localized to the apical and basal sides of cells. However, upon ectopic expression, WIN1 appears on the longitudinal sides of leaf sheath cells, correlated with the appearance of a spiral phenotype in shoots. Despite the spiral phenotype, WIN1-overexpressing plants exhibit a normal phototropic response. Although treatments with exogenous auxins or a polar auxin transport inhibitor do not alter the spiral phenotype, the excurvature side has a higher auxin concentration than the incurvature side. Furthermore, actin filaments are more prominent in the excurvature side than in the incurvature side, which correlates with cell size differences between these two sides. Interestingly, ectopic expression of WIN1 does not cause either unequal auxin distribution or actin filament differences in roots, so a spiral phenotype is not observed in roots. The action of WIN1 appears to be different from that of other proteins causing a spiral phenotype, and it is likely that WIN1 is involved in 1-N-naphthylphthalamic acid-insensitive plasmodesmata-mediated auxin transport.
Collapse
Affiliation(s)
- Ming-Lung Cheng
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - An-Shan Hsiao
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Ya-Fang Hong
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Su-May Yu
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Tuan-Hua David Ho
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| |
Collapse
|
19
|
Hsia MM, O'Malley R, Cartwright A, Nieu R, Gordon SP, Kelly S, Williams TG, Wood DF, Zhao Y, Bragg J, Jordan M, Pauly M, Ecker JR, Gu Y, Vogel JP. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:361-370. [PMID: 28432803 DOI: 10.1111/tpj.13582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 05/07/2023]
Abstract
Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21 165 T-DNA lines, 15 569 of which were produced in this study. This increased the number of unique insertion sites in the T-DNA collection by 21 078, bringing the overall total to 26 112. Thirty-seven per cent (9754) of these insertion sites are within genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene. Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population. To demonstrate the utility of this collection, we phenotypically characterized six T-DNA lines with insertions in genes previously shown in other systems to be involved in cellulose biosynthesis, hemicellulose biosynthesis, secondary cell wall development, DNA damage repair, wax biosynthesis and chloroplast synthesis. In all cases, the phenotypes observed supported previous studies, demonstrating the utility of this collection for plant functional genomics. The Brachypodium T-DNA collection can be accessed at http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/.
Collapse
Affiliation(s)
- Mon Mandy Hsia
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Ronan O'Malley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies and the Howard Hughes Medical Institute, 10010 North Torrey Pines Rd., La Jolla, CA, 92037, USA
- DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
| | - Amy Cartwright
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
- DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
| | - Rita Nieu
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Sean P Gordon
- DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
| | - Sandra Kelly
- Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB, R6M 1Y5, Canada
| | - Tina G Williams
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Delilah F Wood
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Yunjun Zhao
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Jennifer Bragg
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Mark Jordan
- Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB, R6M 1Y5, Canada
| | - Markus Pauly
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies and the Howard Hughes Medical Institute, 10010 North Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Yong Gu
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - John P Vogel
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
- DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
| |
Collapse
|
20
|
Wang P, Karki S, Biswal AK, Lin HC, Dionora MJ, Rizal G, Yin X, Schuler ML, Hughes T, Fouracre JP, Jamous BA, Sedelnikova O, Lo SF, Bandyopadhyay A, Yu SM, Kelly S, Quick WP, Langdale JA. Candidate regulators of Early Leaf Development in Maize Perturb Hormone Signalling and Secondary Cell Wall Formation When Constitutively Expressed in Rice. Sci Rep 2017; 7:4535. [PMID: 28674432 PMCID: PMC5495811 DOI: 10.1038/s41598-017-04361-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/15/2017] [Indexed: 12/22/2022] Open
Abstract
All grass leaves are strap-shaped with a series of parallel veins running from base to tip, but the distance between each pair of veins, and the cell-types that develop between them, differs depending on whether the plant performs C3 or C4 photosynthesis. As part of a multinational effort to introduce C4 traits into rice to boost crop yield, candidate regulators of C4 leaf anatomy were previously identified through an analysis of maize leaf transcriptomes. Here we tested the potential of 60 of those candidate genes to alter leaf anatomy in rice. In each case, transgenic rice lines were generated in which the maize gene was constitutively expressed. Lines grouped into three phenotypic classes: (1) indistinguishable from wild-type; (2) aberrant shoot and/or root growth indicating possible perturbations to hormone homeostasis; and (3) altered secondary cell wall formation. One of the genes in class 3 defines a novel monocot-specific family. None of the genes were individually sufficient to induce C4-like vein patterning or cell-type differentiation in rice. A better understanding of gene function in C4 plants is now needed to inform more sophisticated engineering attempts to alter leaf anatomy in C3 plants.
Collapse
Affiliation(s)
- Peng Wang
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK
| | - Shanta Karki
- International Rice Research Institute, Los Banos, 4030, Laguna, Philippines.,Ministry of Agricultural Development, Government of Nepal, Singhadurbar, Kathmandu, Nepal
| | - Akshaya K Biswal
- International Rice Research Institute, Los Banos, 4030, Laguna, Philippines.,Department of Biology, University North Carolina, Chapel Hill, NC, 27599, USA
| | - Hsiang-Chun Lin
- International Rice Research Institute, Los Banos, 4030, Laguna, Philippines
| | | | - Govinda Rizal
- International Rice Research Institute, Los Banos, 4030, Laguna, Philippines.,Baniyatar-220, Tokha-12, Kathmandu, Nepal
| | - Xiaojia Yin
- International Rice Research Institute, Los Banos, 4030, Laguna, Philippines
| | - Mara L Schuler
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK.,Department of Biology, Heinrich Heine University, D-40225, Düsseldorf, Germany
| | - Tom Hughes
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK
| | - Jim P Fouracre
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK.,Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Basel Abu Jamous
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK
| | - Olga Sedelnikova
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | | | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK
| | - W Paul Quick
- International Rice Research Institute, Los Banos, 4030, Laguna, Philippines
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK.
| |
Collapse
|
21
|
Xiao X, Tang Z, Li X, Hong Y, Li B, Xiao W, Gao Z, Lin D, Li C, Luo L, Niu X, He C, Chen Y. Overexpressing OsMAPK12-1 inhibits plant growth and enhances resistance to bacterial disease in rice. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:694-704. [PMID: 32480599 DOI: 10.1071/fp16397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/29/2017] [Indexed: 06/11/2023]
Abstract
Mitogen-activated protein kinases (MAPKs) play important roles in plant growth and development, plant abiotic stresses signalling pathway and plant-pathogen interactions. However, little is known about the roles of MAPKs in modulating plant growth and pathogen resistance. In this study, we found that OsMAPK12-1, an alternatively spliced form of BWMK1 in rice (Oryza sativa L.), was induced by various elicitors, such as jasmonic acid, salicylic acid, melatonin and bacterial pathogens. To further investigate the involvement of OsMAPK12-1 in plant growth and stress responses to bacterial pathogens, we constructed OsMAPK12-1 overexpression and knockdown (RNAi) transgenic rice lines. Interestingly, overexpressing OsMAP12-1 inhibited seed germination and seedling growth. Additionally, the OsMAP12-1-overexpression lines displayed enhanced disease resistance against Xanthomonas oryzae pv. oryzae PXO99 and Xanthomonas oryzae pv. oryzicola RS105, whereas the OsMAPK12-1-RNAi lines were more susceptible to these pathogens than wild type. These results suggest that OsMAPK12-1 plays a negative role in plant growth and positively modulates disease resistance against bacterial blight and streak in rice.
Collapse
Affiliation(s)
- Xiaorong Xiao
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Zhijuan Tang
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Xiuqiong Li
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Yuhui Hong
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Boling Li
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Wenfang Xiao
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Zhiliang Gao
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Daozhe Lin
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Chunxia Li
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Lijuan Luo
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Xiaolei Niu
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| | - Yinhua Chen
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Hainan University, Haikou 570228, PR China
| |
Collapse
|
22
|
Bi H, Yang B. Gene Editing With TALEN and CRISPR/Cas in Rice. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:81-98. [PMID: 28712502 DOI: 10.1016/bs.pmbts.2017.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Engineered, site-specific nucleases induce genomic double-strand DNA breaks and break repair processes enable genome editing in a plethora of eukaryotic genomes. TALENs (transcription activator-like effector nucleases) and CRISPR/Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) are potent biotechnological tools used for genome editing. In rice, species-tailored editing tools have proven to be efficient and easy to use. Both tools are capable of generating DNA double-strand breaks (DSBs) in vivo and such breaks can be repaired either by error-prone NHEJ (nonhomologous end joining) that leads to nucleotide insertions or deletions or by HDR (homology-directed repair) if an appropriate exogenous DNA template is provided. NHEJ repair often results in gene knockout, while HDR results in precise nucleotide sequence or gene replacement. In this review, we revisit the molecular mechanisms underlying DSB repair in eukaryotes and review the TALEN and CRISPR technologies (CRISPR/Cas9, CRISPR/Cpf1, and Base Editor) developed and utilized for genome editing by scientists in rice community.
Collapse
Affiliation(s)
- Honghao Bi
- Iowa State University, Ames, IA, United States
| | - Bing Yang
- Iowa State University, Ames, IA, United States.
| |
Collapse
|
23
|
Wang Y, Li D, Gao J, Li X, Zhang R, Jin X, Hu Z, Zheng B, Persson S, Chen P. The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively regulates salt stress tolerance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1479-1491. [PMID: 28369540 PMCID: PMC5444449 DOI: 10.1093/jxb/erx061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stress induces changes of modified nucleosides in tRNA, and these changes can influence codon-anticodon interaction and therefore the translation of target proteins. Certain nucleoside modification genes are associated with regulation of stress tolerance and immune response in plants. In this study, we found a dramatic increase of 2'-O-methyladenosine (Am) nucleoside in rice seedlings subjected to salt stress and abscisic acid (ABA) treatment. We identified LOC_Os03g61750 (OsTRM13) as a rice candidate methyltransferase for the Am modification. OsTRM13 transcript levels increased significantly upon salt stress and ABA treatment, and the OsTrm13 protein was found to be located primarily to the nucleus. More importantly, OsTRM13 overexpression plants displayed improved salt stress tolerance, and vice versa, OsTRM13 RNA interference (RNAi) plants showed reduced tolerance. Furthermore, OsTRM13 complemented a yeast trm13Δ mutant, deficient in Am synthesis, and the purified OsTrm13 protein catalysed Am nucleoside formation on tRNA-Gly-GCC in vitro. Our results show that OsTRM13, encoding a rice tRNA nucleoside methyltransferase, is an important regulator of salt stress tolerance in rice.
Collapse
Affiliation(s)
- Youmei Wang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China
| | - Junbao Gao
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xukai Li
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Rui Zhang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xiaohuan Jin
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Zhen Hu
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Bo Zheng
- College of Horticulture and Forestry Sciences, HuaZhong Agricultural University, Wuhan 430070, China
| | - Staffan Persson
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
- School of Biosciences, University of Melbourne, Parkville 3010 VIC, Australia
| | - Peng Chen
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
24
|
Abstract
Plants, like other eukaryotes, have evolved complex mechanisms to coordinate gene expression during development, environmental response, and cellular homeostasis. Transcription factors (TFs), accompanied by basic cofactors and posttranscriptional regulators, are key players in gene-regulatory networks (GRNs). The coordinated control of gene activity is achieved by the interplay of these factors and by physical interactions between TFs and DNA. Here, we will briefly outline recent technological progress made to elucidate GRNs in plants. We will focus on techniques that allow us to characterize physical interactions in GRNs in plants and to analyze their regulatory consequences. Targeted manipulation allows us to test the relevance of specific gene-regulatory interactions. The combination of genome-wide experimental approaches with mathematical modeling allows us to get deeper insights into key-regulatory interactions and combinatorial control of important processes in plants.
Collapse
Affiliation(s)
- Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Dijun Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| |
Collapse
|
25
|
Moin M, Bakshi A, Saha A, Udaya Kumar M, Reddy AR, Rao KV, Siddiq EA, Kirti PB. Activation tagging in indica rice identifies ribosomal proteins as potential targets for manipulation of water-use efficiency and abiotic stress tolerance in plants. PLANT, CELL & ENVIRONMENT 2016; 39:2440-2459. [PMID: 27411514 DOI: 10.1111/pce.12796] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/01/2016] [Accepted: 07/03/2016] [Indexed: 05/23/2023]
Abstract
We have generated 3900 enhancer-based activation-tagged plants, in addition to 1030 stable Dissociator-enhancer plants in a widely cultivated indica rice variety, BPT-5204. Of them, 3000 were screened for water-use efficiency (WUE) by analysing photosynthetic quantum efficiency and yield-related attributes under water-limiting conditions that identified 200 activation-tagged mutants, which were analysed for flanking sequences at the site of enhancer integration in the genome. We have further selected five plants with low Δ13 C, high quantum efficiency and increased plant yield compared with wild type for a detailed investigation. Expression studies of 18 genes in these mutants revealed that in four plants one of the three to four tagged genes became activated, while two genes were concurrently up-regulated in the fifth plant. Two genes coding for proteins involved in 60S ribosomal assembly, RPL6 and RPL23A, were among those that became activated by enhancers. Quantitative expression analysis of these two genes also corroborated the results on activating-tagging. The high up-regulation of RPL6 and RPL23A in various stress treatments and the presence of significant cis-regulatory elements in their promoter regions along with the high up-regulation of several of RPL genes in various stress treatments indicate that they are potential targets for manipulating WUE/abiotic stress tolerance.
Collapse
Affiliation(s)
- Mazahar Moin
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Achala Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - M Udaya Kumar
- Department of Crop Physiology, University of Agricultural Sciences - GKVK, Hebbal, Bangalore, India
| | - Attipalli R Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - K V Rao
- Center for Plant Molecular Biology, Osmania University, Hyderabad, 500007, India
| | - E A Siddiq
- Institute of Agricultural Biotechnology, PJTS Agricultural University, Rajendranagar, Hyderabad, 500030, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India.
| |
Collapse
|
26
|
Wei FJ, Tsai YC, Hsu YM, Chen YA, Huang CT, Wu HP, Huang LT, Lai MH, Kuang LY, Lo SF, Yu SM, Lin YR, Hsing YIC. Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source. PLoS One 2016; 11:e0155768. [PMID: 27186981 PMCID: PMC4871347 DOI: 10.1371/journal.pone.0155768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/03/2016] [Indexed: 01/12/2023] Open
Abstract
Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations.
Collapse
Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Ming Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-An Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ching-Ting Huang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Lin-Yun Kuang
- Transgenic Plant Core Facility, Academia Sinica, Taipei, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yue-Ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
27
|
Wei FJ, Kuang LY, Oung HM, Cheng SY, Wu HP, Huang LT, Tseng YT, Chiou WY, Hsieh-Feng V, Chung CH, Yu SM, Lee LY, Gelvin SB, Hsing YIC. Somaclonal variation does not preclude the use of rice transformants for genetic screening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:648-59. [PMID: 26833589 DOI: 10.1111/tpj.13132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/21/2015] [Accepted: 01/20/2016] [Indexed: 05/07/2023]
Abstract
Rice (Oryza sativa) is one of the world's most important crops. Rice researchers make extensive use of insertional mutants for the study of gene function. Approximately half a million flanking sequence tags from rice insertional mutant libraries are publicly available. However, the relationship between genotype and phenotype is very weak. Transgenic plant assays have been used frequently for complementation, overexpression or antisense analysis, but sequence changes caused by callus growth, Agrobacterium incubation medium, virulence genes, transformation and selection conditions are unknown. We used high-throughput sequencing of DNA from rice lines derived from Tainung 67 to analyze non-transformed and transgenic rice plants for mutations caused by these parameters. For comparison, we also analyzed sequence changes for two additional rice varieties and four T-DNA tagged transformants from the Taiwan Rice Insertional Mutant resource. We identified single-nucleotide polymorphisms, small indels, large deletions, chromosome doubling and chromosome translocations in these lines. Using standard rice regeneration/transformation procedures, the mutation rates of regenerants and transformants were relatively low, with no significant differences among eight tested treatments in the Tainung 67 background and in the cultivars Taikeng 9 and IR64. Thus, we could not conclusively detect sequence changes resulting from Agrobacterium-mediated transformation in addition to those caused by tissue culture-induced somaclonal variation. However, the mutation frequencies within the two publically available tagged mutant populations, including TRIM transformants or Tos17 lines, were about 10-fold higher than the frequency of standard transformants, probably because mass production of embryogenic calli and longer callus growth periods were required to generate these large libraries.
Collapse
Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Lin-Yun Kuang
- Transgenic Plant Core Facility, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Hui-Min Oung
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Sin-Yuan Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Yi-Tzu Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
- Institute of Plant Biology, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Wan-Yi Chiou
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Vicki Hsieh-Feng
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Cheng-Han Chung
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Lan-Ying Lee
- Department of Biological Sciences, Purdue University, 201 South University St., West Lafayette, IN, 47907-1392, USA
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, 201 South University St., West Lafayette, IN, 47907-1392, USA
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| |
Collapse
|