1
|
Zhu C, Zhao L, Zhao S, Niu X, Li L, Gao H, Liu J, Wang L, Zhang T, Cheng R, Shi Z, Zhang H, Wang G. Utilizing machine learning and bioinformatics analysis to identify drought-responsive genes affecting yield in foxtail millet. Int J Biol Macromol 2024; 277:134288. [PMID: 39079238 DOI: 10.1016/j.ijbiomac.2024.134288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024]
Abstract
Drought stress is a major constraint on crop development, potentially causing huge yield losses and threatening global food security. Improving Crop's stress tolerance is usually associated with a yield penalty. One way to balance yield and stress tolerance is modification specific gene by emerging precision genome editing technology. However, our knowledge of yield-related drought-tolerant genes is still limited. Foxtail millet (Setaria italica) has a remarkable tolerance to drought and is considered to be a model C4 crop that is easy to engineer. Here, we have identified 46 drought-responsive candidate genes by performing a machine learning-based transcriptome study on two drought-tolerant and two drought-sensitive foxtail millet cultivars. A total of 12 important drought-responsive genes were screened out by principal component analysis and confirmed experimentally by qPCR. Significantly, by investigating the haplotype of these genes based on 1844 germplasm resources, we found two genes (Seita.5G251300 and Seita.8G036300) exhibiting drought-tolerant haplotypes that possess an apparent advantage in 1000 grain weight and main panicle grain weight without penalty in grain weight per plant. These results demonstrate the potential of Seita.5G251300 and Seita.8G036300 for breeding drought-tolerant high-yielding foxtail millet. It provides important insights for the breeding of drought-tolerant high-yielding crop cultivars through genetic manipulation technology.
Collapse
Affiliation(s)
- Chunhui Zhu
- College of Physics, Hebei Normal University, Shijiazhuang 050024, China.
| | - Ling Zhao
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Shaoxing Zhao
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Xingfang Niu
- College of Physics, Hebei Normal University, Shijiazhuang 050024, China; College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Lin Li
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Hui Gao
- Hebei Key Laboratory of Crop Stress Biology, Department of Life Science and Technology, College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Jiaxin Liu
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China; Hebei Key Laboratory of Crop Stress Biology, Department of Life Science and Technology, College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Litao Wang
- College of Physics, Hebei Normal University, Shijiazhuang 050024, China; College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Ting Zhang
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Ruhong Cheng
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Zhigang Shi
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Haoshan Zhang
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China.
| | - Genping Wang
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs, National Foxtail Millet Improvement Center, Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China.
| |
Collapse
|
2
|
Gal A, Dalal A, Anfang M, Sharma D, Binenbaum J, Muchaki P, Kumar R, Egbaria A, Duarte KE, Kelly G, de Souza WR, Sade N. Plasma membrane aquaporins regulate root hydraulic conductivity in the model plant Setaria viridis. PLANT PHYSIOLOGY 2023; 193:2640-2660. [PMID: 37607257 DOI: 10.1093/plphys/kiad469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023]
Abstract
The high rate of productivity observed in panicoid crops is in part due to their extensive root system. Recently, green foxtail (Setaria viridis) has emerged as a genetic model system for panicoid grasses. Natural accessions of S. viridis originating from different parts of the world, with differential leaf physiological behavior, have been identified. This work focused on understanding the physiological and molecular mechanisms controlling root hydraulic conductivity and root-to-shoot gas exchange signaling in S. viridis. We identified 2 accessions, SHA and ZHA, with contrasting behavior at the leaf, root, and whole-plant levels. Our results indicated a role for root aquaporin (AQP) plasma membrane (PM) intrinsic proteins in the differential behavior of SHA and ZHA. Moreover, a different root hydraulic response to low levels of abscisic acid between SHA and ZHA was observed, which was associated with root AQPs. Using cell imaging, biochemical, and reverse genetic approaches, we identified PM intrinsic protein 1;6 (PIP1;6) as a possible PIP1 candidate that regulates radial root hydraulics and root-to-shoot signaling of gas exchange in S. viridis. In heterologous systems, PIP1;6 localized in the endoplasmic reticulum, and upon interaction with PIP2s, relocalization to the PM was observed. PIP1;6 was predominantly expressed at the root endodermis. Generation of knockout PIP1;6 plants (KO-PIP1;6) in S. viridis showed altered root hydraulic conductivity, altered gas exchange, and alteration of root transcriptional patterns. Our results indicate that PIPs are essential in regulating whole-plant water homeostasis in S. viridis. We conclude that root hydraulic conductivity and gas exchange are positively associated and are regulated by AQPs.
Collapse
Affiliation(s)
- Atara Gal
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ahan Dalal
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moran Anfang
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jenia Binenbaum
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Purity Muchaki
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rakesh Kumar
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Aiman Egbaria
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Karoline Estefani Duarte
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André 09210170, Brazil
| | - Gilor Kelly
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization, Rishon Le-Zion 7505101, Israel
| | - Wagner Rodrigo de Souza
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André 09210170, Brazil
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
3
|
Meng Q, Zhang R, Wang Y, Zhi H, Tang S, Jia G, Diao X. Genome-Wide Characterization and Haplotypic Variation Analysis of the YUC Gene Family in Foxtail Millet ( Setaria italica). Int J Mol Sci 2023; 24:15637. [PMID: 37958621 PMCID: PMC10648439 DOI: 10.3390/ijms242115637] [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: 09/04/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023] Open
Abstract
Panicle development and grain production in crop species are essential breeding characteristics affected by the synthesis of auxin, which is influenced by flavin monooxygenase-encoding genes such as YUC (YUCCA) family members. In this trial, fourteen YUCs were identified and named uniformly in foxtail millet, an ancient crop species cultivated across the world. The phylogenetic analysis revealed that the SiYUCs were clustered into four subgroups; protein motif and gene structure analyses suggested that the closely clustered SiYUC genes were relatively conserved within each subgroup; while genome mapping analysis indicated that the SiYUC genes were unevenly distributed on foxtail millet chromosomes and colinear with other grass species. Transcription analysis revealed that the SiYUC genes differed greatly in expression pattern in different tissues and contained hormonal/light/stress-responding cis-elements. The haplotype characterization of SiYUC genes indicated many superior haplotypes of SiYUCs correlated with higher panicle and grain weight could be favorably selected by breeding. These results will be useful for the further study of the functional characteristics of SiYUC genes, particularly with regard to the marker-assisted pyramiding of beneficial haplotypes in foxtail millet breeding programs.
Collapse
Affiliation(s)
| | | | | | | | | | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.M.); (R.Z.); (Y.W.); (H.Z.); (S.T.)
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.M.); (R.Z.); (Y.W.); (H.Z.); (S.T.)
| |
Collapse
|
4
|
Zhao M, Zhang Q, Liu H, Tang S, Shang C, Zhang W, Sui Y, Zhang Y, Zheng C, Zhang H, Liu C, Chu J, Jia G, Wang H, Liu X, An D, Zhu F, Zhi H, Wu C, Diao X. The osmotic stress-activated receptor-like kinase DPY1 mediates SnRK2 kinase activation and drought tolerance in Setaria. THE PLANT CELL 2023; 35:3782-3808. [PMID: 37462269 PMCID: PMC10533336 DOI: 10.1093/plcell/koad200] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/25/2023] [Indexed: 09/29/2023]
Abstract
Plant genomes encode many receptor-like kinases (RLKs) that localize to the cell surface and perceive a wide variety of environmental cues to initiate downstream signaling cascades. Whether these RLKs participate in dehydration stress signaling in plants is largely unknown. DROOPY LEAF1 (DPY1), a leucine-rich repeat (LRR)-RLK, was recently shown to regulate plant architecture by orchestrating early brassinosteroid signaling in foxtail millet (Setaria italica). Here, we show that DPY1 is essential for the acclimation of foxtail millet to drought stress. DPY1 can be phosphorylated and activated in response to osmotic stress and is required for more than half of osmotic stress-induced global phosphorylation events, including the phosphorylation of sucrose nonfermenting kinase 2s (SnRK2s), the central kinases involved in osmotic stress. DPY1 acts upstream of STRESS-ACTIVATED PROTEIN KINASE 6 (SAPK6, a subclass I SnRK2) and is required for full SAPK6 activation, thereby allowing regulation of downstream genes to mount a response against drought stress. These signaling events are largely independent of DPY1-mediated brassinosteroid signaling. The DPY1-SAPK6 module is specific to seed plants and is absent in ancestral nonseed plants. Our findings reveal a dehydration stress-activated RLK that plays an indispensable role in osmotic stress signaling and mediates SnRK2 activation at the cell surface.
Collapse
Affiliation(s)
- Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Qi Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Hong Liu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunyue Shang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuxue Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Chunyan Zheng
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Shijiazhuang 050024, China
| | - Diaoguo An
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Shijiazhuang 050024, China
| |
Collapse
|
5
|
Gong L, Li B, Zhu T, Xue B. Genome-wide identification and expression profiling analysis of DIR gene family in Setaria italica. FRONTIERS IN PLANT SCIENCE 2023; 14:1243806. [PMID: 37799547 PMCID: PMC10548141 DOI: 10.3389/fpls.2023.1243806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023]
Abstract
Dirigent (DIR) proteins play essential roles in regulating plant growth and development, as well as enhancing resistance to abiotic and biotic stresses. However, the whole-genome identification and expression profiling analysis of DIR gene family in millet (Setaria italica (Si)) have not been systematically understood. In this study, we conducted genome-wide identification and expression analysis of the S. italica DIR gene family, including gene structures, conserved domains, evolutionary relationship, chromosomal locations, cis-elements, duplication events, gene collinearity and expression patterns. A total of 38 SiDIR members distributed on nine chromosomes were screened and identified. SiDIR family members in the same group showed higher sequence similarity. The phylogenetic tree divided the SiDIR proteins into six subfamilies: DIR-a, DIR-b/d, DIR-c, DIR-e, DIR-f, and DIR-g. According to the tertiary structure prediction, DIR proteins (like SiDIR7/8/9) themselves may form a trimer to exert function. The result of the syntenic analysis showed that tandem duplication may play the major driving force during the evolution of SiDIRs. RNA-seq data displayed higher expression of 16 SiDIR genes in root tissues, and this implied their potential functions during root development. The results of quantitative real-time PCR (RT-qPCR) assays revealed that SiDIR genes could respond to the stress of CaCl2, CdCl, NaCl, and PEG6000. This research shed light on the functions of SiDIRs in responding to abiotic stress and demonstrated their modulational potential during root development. In addition, the membrane localization of SiDIR7/19/22 was confirmed to be consistent with the forecast. The results above will provide a foundation for further and deeper investigation of DIRs.
Collapse
Affiliation(s)
- Luping Gong
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Bingbing Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Tao Zhu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Baoping Xue
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
6
|
Wu C, Guo D. Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution. Int J Mol Sci 2023; 24:14165. [PMID: 37762466 PMCID: PMC10531853 DOI: 10.3390/ijms241814165] [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: 07/09/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and adaptation to extreme environmental conditions, but the mechanisms behind the assembly of C4 machinery remain elusive. This study attempts to dissect the evolutionary divergence from C3 to C4 photosynthesis in five photosynthetic model plants from the grass family, using a combined comparative transcriptomics and deep learning technology. By examining and comparing gene expression levels in bundle sheath and mesophyll cells of five model plants, we identified 16 differentially expressed signature genes showing cell-specific expression patterns in C3 and C4 plants. Among them, two showed distinctively opposite cell-specific expression patterns in C3 vs. C4 plants (named as FOGs). The in silico physicochemical analysis of the two FOGs illustrated that C3 homologous proteins of LHCA6 had low and stable pI values of ~6, while the pI values of LHCA6 homologs increased drastically in C4 plants Setaria viridis (7), Zea mays (8), and Sorghum bicolor (over 9), suggesting this protein may have different functions in C3 and C4 plants. Interestingly, based on pairwise protein sequence/structure similarities between each homologous FOG protein, one FOG PGRL1A showed local inconsistency between sequence similarity and structure similarity. To find more examples of the evolutionary characteristics of FOG proteins, we investigated the protein sequence/structure similarities of other FOGs (transcription factors) and found that FOG proteins have diversified incompatibility between sequence and structure similarities during grass family evolution. This raised an interesting question as to whether the sequence similarity is related to structure similarity during C4 photosynthesis evolution.
Collapse
Affiliation(s)
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China;
| |
Collapse
|
7
|
Liu Q, Teng S, Deng C, Wu S, Li H, Wang Y, Wu J, Cui X, Zhang Z, Quick WP, Brutnell TP, Sun X, Lu T. SHORT ROOT and INDETERMINATE DOMAIN family members govern PIN-FORMED expression to regulate minor vein differentiation in rice. THE PLANT CELL 2023; 35:2848-2870. [PMID: 37154077 PMCID: PMC10396363 DOI: 10.1093/plcell/koad125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/08/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023]
Abstract
C3 and C4 grasses directly and indirectly provide the vast majority of calories to the human diet, yet our understanding of the molecular mechanisms driving photosynthetic productivity in grasses is largely unexplored. Ground meristem cells divide to form mesophyll or vascular initial cells early in leaf development in C3 and C4 grasses. Here we define a genetic circuit composed of SHORT ROOT (SHR), INDETERMINATE DOMAIN (IDD), and PIN-FORMED (PIN) family members that specifies vascular identify and ground cell proliferation in leaves of both C3 and C4 grasses. Ectopic expression and loss-of-function mutant studies of SHR paralogs in the C3 plant Oryza sativa (rice) and the C4 plant Setaria viridis (green millet) revealed the roles of these genes in both minor vein formation and ground cell differentiation. Genetic and in vitro studies further suggested that SHR regulates this process through its interactions with IDD12 and 13. We also revealed direct interactions of these IDD proteins with a putative regulatory element within the auxin transporter gene PIN5c. Collectively, these findings indicate that a SHR-IDD regulatory circuit mediates auxin transport by negatively regulating PIN expression to modulate minor vein patterning in the grasses.
Collapse
Affiliation(s)
- Qiming Liu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Shouzhen Teng
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Chen Deng
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Suting Wu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Haoshu Li
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Yanwei Wang
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Jinxia Wu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Xuean Cui
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Zhiguo Zhang
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - William Paul Quick
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
- C4 Rice Centre, International Rice Research Institute, Los Banos, Laguna 4030, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Thomas P Brutnell
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Xuehui Sun
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Tiegang Lu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| |
Collapse
|
8
|
Gao H, Suo X, Zhao L, Ma X, Cheng R, Wang G, Zhang H. Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum. PLANT CELL REPORTS 2023; 42:1003-1024. [PMID: 37012438 DOI: 10.1007/s00299-023-03009-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE This paper sheds light on the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 maybe involved in the ABA-dependent pathway of drought response. The MADS gene family is a key regulatory factor family that controls growth, reproduction, and response to abiotic stress in plants. However, the molecular evolution of this family is rarely reported. Here, a total of 265 MADS genes were identified in Setaria italica (foxtail millet), Setaria viridis (green millet), and Panicum virgatum (switchgrass) and analyzed by bioinformatics, including physicochemical characteristics, subcellular localization, chromosomal position and duplicate, motif distribution, genetic structure, genetic evolvement, and expression patterns. Phylogenetic analysis was used to categorize these genes into M and MIKC types. The distribution of motifs and gene structure were similar for the corresponding types. According to a collinearity study, the MADS genes have been mostly conserved during evolution. The principal cause of their expansion is segmental duplication. However, the MADS gene family tends to shrink in foxtail millet, green millet, and switchgrass. The MADS genes were subjected to purifying selection, but several positive selection sites were also identified in three species. And most of the promoters of MADS genes contain cis-elements related to stress and hormonal response. RNA-seq and quantitative Real-time PCR (qRT-PCR) analysis also were examined. SiMADS genes expression levels are considerably changed in reaction to various treatments, following qRT-PCR analysis. This sheds fresh light on the evolution and expansion of the MADS family in foxtail millet, green millet, and switchgrass, and lays the foundation for further research on their functions.
Collapse
Affiliation(s)
- Hui Gao
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiaoman Suo
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ling Zhao
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xinlei Ma
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Haoshan Zhang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
- Chinese Academy of Agricultural Sciences Institute of Crop Sciences, Beijing, 100081, China.
| |
Collapse
|
9
|
Tang S, Zhao Z, Liu X, Sui Y, Zhang D, Zhi H, Gao Y, Zhang H, Zhang L, Wang Y, Zhao M, Li D, Wang K, He Q, Zhang R, Zhang W, Jia G, Tang W, Ye X, Wu C, Diao X. An E2-E3 pair contributes to seed size control in grain crops. Nat Commun 2023; 14:3091. [PMID: 37248257 DOI: 10.1038/s41467-023-38812-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
Understanding the molecular mechanisms that regulate grain yield is important for improving agricultural productivity. Protein ubiquitination controls various aspects of plant growth but lacks understanding on how E2-E3 enzyme pairs impact grain yield in major crops. Here, we identified a RING-type E3 ligase SGD1 and its E2 partner SiUBC32 responsible for grain yield control in Setaria italica. The conserved role of SGD1 was observed in wheat, maize, and rice. Furthermore, SGD1 ubiquitinates the brassinosteroid receptor BRI1, stabilizing it and promoting plant growth. Overexpression of an elite SGD1 haplotype improved grain yield by about 12.8% per plant, and promote complex biological processes such as protein processing in endoplasmic reticulum, stress responses, photosystem stabilization, and nitrogen metabolism. Our research not only identifies the SiUBC32-SGD1-BRI1 genetic module that contributes to grain yield improvement but also provides a strategy for exploring key genes controlling important traits in Poaceae crops using the Setaria model system.
Collapse
Affiliation(s)
- Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiying Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotong Liu
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural, Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dandan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanzhu Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Linlin Zhang
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yannan Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural, Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Dongdong Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ke Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Renliang Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenqiang Tang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
10
|
Chen L, Ganguly DR, Shafik SH, Danila F, Grof CPL, Sharwood RE, Furbank RT. The role of SWEET4 proteins in the post-phloem sugar transport pathway of Setaria viridis sink tissues. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2968-2986. [PMID: 36883216 PMCID: PMC10560085 DOI: 10.1093/jxb/erad076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/06/2023] [Indexed: 05/21/2023]
Abstract
In the developing seeds of all higher plants, filial cells are symplastically isolated from the maternal tissue supplying photosynthate to the reproductive structure. Photoassimilates must be transported apoplastically, crossing several membrane barriers, a process facilitated by sugar transporters. Sugars Will Eventually be Exported Transporters (SWEETs) have been proposed to play a crucial role in apoplastic sugar transport during phloem unloading and the post-phloem pathway in sink tissues. Evidence for this is presented here for developing seeds of the C4 model grass Setaria viridis. Using immunolocalization, SvSWEET4 was detected in various maternal and filial tissues within the seed along the sugar transport pathway, in the vascular parenchyma of the pedicel, and in the xylem parenchyma of the stem. Expression of SvSWEET4a in Xenopus laevis oocytes indicated that it functions as a high-capacity glucose and sucrose transporter. Carbohydrate and transcriptional profiling of Setaria seed heads showed that there were some developmental shifts in hexose and sucrose content and consistent expression of SvSWEET4 homologues. Collectively, these results provide evidence for the involvement of SWEETs in the apoplastic transport pathway of sink tissues and allow a pathway for post-phloem sugar transport into the seed to be proposed.
Collapse
Affiliation(s)
- Lily Chen
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales 2753, Australia
| | - Diep R Ganguly
- Research School of Biology, ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australian Capital Territory 2601, Australia
| | - Sarah H Shafik
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Florence Danila
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Christopher P L Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering Science and Environment, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales 2753, Australia
| | - Robert T Furbank
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| |
Collapse
|
11
|
Li X, Hou S, Feng M, Xia R, Li J, Tang S, Han Y, Gao J, Wang X. MDSi: Multi-omics Database for Setaria italica. BMC PLANT BIOLOGY 2023; 23:223. [PMID: 37101150 PMCID: PMC10134609 DOI: 10.1186/s12870-023-04238-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Foxtail millet (Setaria italica) harbors the small diploid genome (~ 450 Mb) and shows the high inbreeding rate and close relationship to several major foods, feed, fuel and bioenergy grasses. Previously, we created a mini foxtail millet, xiaomi, with an Arabidopsis-like life cycle. The de novo assembled genome data with high-quality and an efficient Agrobacterium-mediated genetic transformation system made xiaomi an ideal C4 model system. The mini foxtail millet has been widely shared in the research community and as a result there is a growing need for a user-friendly portal and intuitive interface to perform exploratory analysis of the data. RESULTS Here, we built a Multi-omics Database for Setaria italica (MDSi, http://sky.sxau.edu.cn/MDSi.htm ), that contains xiaomi genome of 161,844 annotations, 34,436 protein-coding genes and their expression information in 29 different tissues of xiaomi (6) and JG21 (23) samples that can be showed as an Electronic Fluorescent Pictograph (xEFP) in-situ. Moreover, the whole-genome resequencing (WGS) data of 398 germplasms, including 360 foxtail millets and 38 green foxtails and the corresponding metabolic data were available in MDSi. The SNPs and Indels of these germplasms were called in advance and can be searched and compared in an interactive manner. Common tools including BLAST, GBrowse, JBrowse, map viewer, and data downloads were implemented in MDSi. CONCLUSION The MDSi constructed in this study integrated and visualized data from three levels of genomics, transcriptomics and metabolomics, and also provides information on the variation of hundreds of germplasm resources that can satisfies the mainstream requirements and supports the corresponding research community.
Collapse
Affiliation(s)
- Xukai Li
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, Shanxi, 030031, China
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Siyu Hou
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, Shanxi, 030031, China
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Mengmeng Feng
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Rui Xia
- South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Jiawei Li
- South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanhuai Han
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, Shanxi, 030031, China
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Jianhua Gao
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, Shanxi, 030031, China.
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Xingchun Wang
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, Shanxi, 030031, China.
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| |
Collapse
|
12
|
Ermakova M, Lopez-Calcagno PE, Furbank RT, Raines CA, von Caemmerer S. Increased sedoheptulose-1,7-bisphosphatase content in Setaria viridis does not affect C4 photosynthesis. PLANT PHYSIOLOGY 2023; 191:885-893. [PMID: 36282540 PMCID: PMC9922425 DOI: 10.1093/plphys/kiac484] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/28/2022] [Indexed: 05/05/2023]
Abstract
Sedoheptulose-1,7-bisphosphatase (SBPase) is one of the rate-limiting enzymes of the Calvin cycle, and increasing the abundance of SBPase in C3 plants provides higher photosynthetic rates and stimulates biomass and yield. C4 plants usually have higher photosynthetic rates because they operate a biochemical CO2-concentrating mechanism between mesophyll and bundle sheath cells. In the C4 system, SBPase and other enzymes of the Calvin cycle are localized to the bundle sheath cells. Here we tested what effect increasing abundance of SBPase would have on C4 photosynthesis. Using green foxtail millet (Setaria viridis), a model C4 plant of NADP-ME subtype, we created transgenic plants with 1.5 to 3.2 times higher SBPase content compared to wild-type plants. Transcripts of the transgene were found predominantly in the bundle sheaths suggesting the correct cellular localization of the protein. The abundance of ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit was not affected in transgenic plants overexpressing SBPase, and neither was leaf chlorophyll content or photosynthetic electron transport parameters. We found no association between SBPase content in S. viridis and saturating rates of CO2 assimilation. Moreover, a detailed analysis of CO2 assimilation rates at different CO2 partial pressures, irradiances, and leaf temperatures showed no improvement of photosynthesis in plants overexpressing SBPase. We discuss the potential implications of these results for understanding the role of SBPase in regulation of C4 photosynthesis.
Collapse
Affiliation(s)
- Maria Ermakova
- Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Canberra 2600, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Patricia E Lopez-Calcagno
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
- School of Natural and Environmental Sciences, Newcastle University, Newcastle NE1 7RU, UK
| | - Robert T Furbank
- Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Canberra 2600, Australia
| | - Christine A Raines
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Susanne von Caemmerer
- Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Canberra 2600, Australia
| |
Collapse
|
13
|
Liang H, He Q, Zhang H, Zhi H, Tang S, Wang H, Meng Q, Jia G, Chang J, Diao X. Identification and haplotype analysis of SiCHLI: a gene for yellow-green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:24. [PMID: 36739566 DOI: 10.1007/s00122-023-04309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
We cloned and developed functional markers for the SiCHLI gene, which is responsible for the yellow-green color of leaves in foxtail millet, a frequently used marker trait in the hybrid breeding of foxtail millet by using bulked segregant analysis sequencing and haplotype analysis on the F2 and core-collected nature populations. The color of leaves has been widely used as a marker for the hybrid breeding of foxtail millet; however, few related gene have been cloned to date. Here, we used two F2 populations generated from crosses between the highly male-sterile material 125A with yellow-green leaves, and CG58 and S410, which have green leaves, to identify the genes underlying the yellow-green color of the leaves of foxtail millet. The leaves of 125A seedlings were yellow-green, but they became green at the heading stage. The content of chlorophyll a and chlorophyll b was lower, the number of thylakoid lamellae and grana was reduced, and the chloroplasts was more rounded in 125A than in S410 at the yellow-green leaf stage; however, no differences were observed between 125A and S410 in these traits and photosynthetic at the heading stage. Bulked segregant analysis and map-based cloning revealed that the SiCHLI gene is responsible for the leaf colors of 125A. A nonsynonymous mutation (C/T) in exon 3 causes yellow-green leaves in 125A at the seedling stage. Haplotype analysis of the SiCHLI gene in 596 core collected accessions revealed a new haplotype associated with high photosynthetic metabolic potential at the heading and mature stages, which could be used to enhance sterile lines with yellow-green leaves. We developed a functional marker that will facilitate the identification of foxtail millet accessions with the different types of yellow-green leaves. Generally, our study provides new genetic resources to guide the future marker-assisted or target-base editing in foxtail millet hybrid breeding.
Collapse
Affiliation(s)
- Hongkai Liang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Qiang Meng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Jinhua Chang
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China.
| |
Collapse
|
14
|
Wu C, Guo D. Computational Docking Reveals Co-Evolution of C4 Carbon Delivery Enzymes in Diverse Plants. Int J Mol Sci 2022; 23:12688. [PMID: 36293547 PMCID: PMC9604239 DOI: 10.3390/ijms232012688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins are modular functionalities regulating multiple cellular activities in prokaryotes and eukaryotes. As a consequence of higher plants adapting to arid and thermal conditions, C4 photosynthesis is the carbon fixation process involving multi-enzymes working in a coordinated fashion. However, how these enzymes interact with each other and whether they co-evolve in parallel to maintain interactions in different plants remain elusive to date. Here, we report our findings on the global protein co-evolution relationship and local dynamics of co-varying site shifts in key C4 photosynthetic enzymes. We found that in most of the selected key C4 photosynthetic enzymes, global pairwise co-evolution events exist to form functional couplings. Besides, protein-protein interactions between these enzymes may suggest their unknown functionalities in the carbon delivery process. For PEPC and PPCK regulation pairs, pocket formation at the interactive interface are not necessary for their function. This feature is distinct from another well-known regulation pair in C4 photosynthesis, namely, PPDK and PPDK-RP, where the pockets are necessary. Our findings facilitate the discovery of novel protein regulation types and contribute to expanding our knowledge about C4 photosynthesis.
Collapse
Affiliation(s)
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| |
Collapse
|
15
|
Pradhan B, Panda D, Bishi SK, Chakraborty K, Muthusamy SK, Lenka SK. Progress and prospects of C 4 trait engineering in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:920-931. [PMID: 35727191 DOI: 10.1111/plb.13446] [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: 01/14/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Incorporating C4 photosynthetic traits into C3 crops is a rational approach for sustaining future demands for crop productivity. Using classical plant breeding, engineering this complex trait is unlikely to achieve its target. Therefore, it is critical and timely to implement novel biotechnological crop improvement strategies to accomplish this goal. However, a fundamental understanding of C3 , C4 , and C3 -C4 intermediate metabolism is crucial for the targeted use of biotechnological tools. This review assesses recent progress towards engineering C4 photosynthetic traits in C3 crops. We also discuss lessons learned from successes and failures of recent genetic engineering attempts in C3 crops, highlighting the pros and cons of using rice as a model plant for short-, medium- and long-term goals of genetic engineering. This review provides an integrated approach towards engineering improved photosynthetic efficiency in C3 crops for sustaining food, fibre and fuel production around the globe.
Collapse
Affiliation(s)
- B Pradhan
- Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Kolkata, India
| | - D Panda
- Department of Biodiversity & Conservation of Natural Resources, Central University of Odisha, Koraput, India
| | - S K Bishi
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - K Chakraborty
- Department of Plant Physiology, ICAR-National Rice Research Institute, Cuttack, India
| | - S K Muthusamy
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - S K Lenka
- Department of Plant Biotechnology, Gujarat Biotechnology University, Gujarat, India
| |
Collapse
|
16
|
Om K, Arias NN, Jambor CC, MacGregor A, Rezachek AN, Haugrud C, Kunz HH, Wang Z, Huang P, Zhang Q, Rosnow J, Brutnell TP, Cousins AB, Chastain CJ. Pyruvate, phosphate dikinase regulatory protein impacts light response of C4 photosynthesis in Setaria viridis. PLANT PHYSIOLOGY 2022; 190:1117-1133. [PMID: 35876823 PMCID: PMC9516741 DOI: 10.1093/plphys/kiac333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
In C4 plants, the pyruvate (Pyr), phosphate dikinase regulatory protein (PDRP) regulates the activity of the C4 pathway enzyme Pyr, phosphate dikinase (PPDK) in a light-/dark-dependent manner. The importance of this regulatory action to C4 pathway function and overall C4 photosynthesis is unknown. To resolve this question, we assessed in vivo PPDK phospho-regulation and whole leaf photophysiology in a CRISPR-Cas9 PDRP knockout (KO) mutant of the NADP-ME C4 grass green millet (Setaria viridis). PDRP enzyme activity was undetectable in leaf extracts from PDRP KO lines. Likewise, PPDK phosphorylated at the PDRP-regulatory Thr residue was immunologically undetectable in leaf extracts. PPDK enzyme activity in rapid leaf extracts was constitutively high in the PDRP KO lines, irrespective of light or dark pretreatment of leaves. Gas exchange analysis of net CO2 assimilation revealed PDRP KO leaves had markedly slower light induction kinetics when leaves transition from dark to high-light or low-light to high-light. In the initial 30 min of the light induction phase, KO leaves had an ∼15% lower net CO2 assimilation rate versus the wild-type (WT). Despite the impaired slower induction kinetics, we found growth and vigor of the KO lines to be visibly indistinguishable from the WT when grown in normal air and under standard growth chamber conditions. However, the PDRP KO plants grown under a fluctuating light regime exhibited a gradual multi-day decline in Fv/Fm, indicative of progressive photosystem II damage due to the absence of PDRP. Collectively, our results demonstrate that one of PDRP's functions in C4 photosynthesis is to ensure optimal photosynthetic light induction kinetics during dynamic changes in incident light.
Collapse
Affiliation(s)
- Kuenzang Om
- School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236, USA
| | - Nico N Arias
- Department of Biosciences, Minnesota State University-Moorhead, Moorhead, Minnesota 56563, USA
| | - Chaney C Jambor
- Department of Biosciences, Minnesota State University-Moorhead, Moorhead, Minnesota 56563, USA
| | - Alexandra MacGregor
- Department of Biosciences, Minnesota State University-Moorhead, Moorhead, Minnesota 56563, USA
| | - Ashley N Rezachek
- Department of Biosciences, Minnesota State University-Moorhead, Moorhead, Minnesota 56563, USA
| | - Carlan Haugrud
- Department of Biosciences, Minnesota State University-Moorhead, Moorhead, Minnesota 56563, USA
| | | | - Zhonghui Wang
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | | | - Quan Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Josh Rosnow
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | | | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236, USA
| | | |
Collapse
|
17
|
Bellasio C, Ermakova M. Reduction of bundle sheath size boosts cyclic electron flow in C 4 Setaria viridis acclimated to low light. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1223-1237. [PMID: 35866447 PMCID: PMC9545969 DOI: 10.1111/tpj.15915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 05/22/2023]
Abstract
When C4 leaves are exposed to low light, the CO2 concentration in the bundle sheath (BS) cells decreases, causing an increase in photorespiration relative to assimilation, and a consequent reduction in biochemical efficiency. These effects can be mitigated by complex acclimation syndromes, which are of primary importance for crop productivity but are not well studied. We unveil an acclimation strategy involving the coordination of electron transport processes. First, we characterize the anatomy, gas exchange and electron transport of C4 Setaria viridis grown under low light. Through a purposely developed biochemical model, we resolve the photon fluxes and reaction rates to explain how the concerted acclimation strategies sustain photosynthetic efficiency. Our results show that a smaller BS in low-light-grown plants limited leakiness (the ratio of CO2 leak rate out of the BS over the rate of supply via C4 acid decarboxylation) but sacrificed light harvesting and ATP production. To counter ATP shortage and maintain high assimilation rates, plants facilitated light penetration through the mesophyll and upregulated cyclic electron flow in the BS. This shade tolerance mechanism, based on the optimization of light reactions, is possibly more efficient than the known mechanisms involving the rearrangement of carbon metabolism, and could potentially lead to innovative strategies for crop improvement.
Collapse
Affiliation(s)
- Chandra Bellasio
- Department of BiologyUniversity of the Balearic Islands07122PalmaIlles BalearsSpain
- Centre of Excellence for Translational Photosynthesis, Research School of BiologyThe Australian National UniversityActonACT2601Australia
| | - Maria Ermakova
- Centre of Excellence for Translational Photosynthesis, Research School of BiologyThe Australian National UniversityActonACT2601Australia
| |
Collapse
|
18
|
Genome‑wide identification, phylogenetic and expression pattern analysis of GATA family genes in foxtail millet (Setaria italica). BMC Genomics 2022; 23:549. [PMID: 35918632 PMCID: PMC9347092 DOI: 10.1186/s12864-022-08786-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/18/2022] [Indexed: 11/27/2022] Open
Abstract
Background Transcription factors (TFs) play important roles in plants. Among the major TFs, GATA plays a crucial role in plant development, growth, and stress responses. However, there have been few studies on the GATA gene family in foxtail millet (Setaria italica). The release of the foxtail millet reference genome presents an opportunity for the genome-wide characterization of these GATA genes. Results In this study, we identified 28 GATA genes in foxtail millet distributed on seven chromosomes. According to the classification method of GATA members in Arabidopsis, SiGATA was divided into four subfamilies, namely subfamilies I, II, III, and IV. Structural analysis of the SiGATA genes showed that subfamily III had more introns than other subfamilies, and a large number of cis-acting elements were abundant in the promoter region of the SiGATA genes. Three tandem duplications and five segmental duplications were found among SiGATA genes. Tissue-specific results showed that the SiGATA genes were mainly expressed in foxtail millet leaves, followed by peels and seeds. Many genes were significantly induced under the eight abiotic stresses, such as SiGATA10, SiGATA16, SiGATA18, and SiGATA25, which deserve further attention. Conclusions Collectively, these findings will be helpful for further in-depth studies of the biological function of SiGATA, and will provide a reference for the future molecular breeding of foxtail millet. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08786-0.
Collapse
|
19
|
Duarte KE, Basso MF, de Oliveira NG, da Silva JCF, de Oliveira Garcia B, Cunha BADB, Cardoso TB, Nepomuceno AL, Kobayashi AK, Santiago TR, de Souza WR, Molinari HBC. MicroRNAs expression profiles in early responses to different levels of water deficit in Setaria viridis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1607-1624. [PMID: 36389096 PMCID: PMC9530107 DOI: 10.1007/s12298-022-01226-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Water deficit is a major constraint for crops of economic importance in almost all agricultural regions. However, plants have an active defense system to adapt to these adverse conditions, acting in the reprogramming of gene expression responsible for encoding microRNAs (miRNAs). These miRNAs promote the regulation to the target gene expression by the post-transcriptional (PTGS) and transcriptional gene silencing (TGS), modulating several pathways including defense response to water deficit. The broader knowledge of the miRNA expression profile and its regulatory networks in response to water deficit can provide evidence for the development of new biotechnological tools for genetic improvement of several important crops. In this study, we used Setaria viridis accession A10.1 as a C4 model plant to widely investigate the miRNA expression profile in early responses to different levels of water deficit. Ecophysiological studies in Setaria viridis under water deficit and after rewatering demonstrated a drought tolerant accession, capable of a rapid recovery from the stress. Deep small RNA sequencing and degradome studies were performed in plants submitted to drought to identify differentially expressed miRNA genes and their predicted targets, using in silico analysis. Our findings showed that several miRNAs were differentially modulated in response to distinctive levels of water deficit and after rewatering. The predicted mRNA targets mainly corresponded to genes related to cell wall remodeling, antioxidant system and drought-related transcription factors, indicating that these genes are rapidly regulated in early responses to drought stress. The implications of these modulations are extensively discussed, and higher-effect miRNAs are suggested as major players for potential use in genetic engineering to improve drought tolerance in economically important crops, such as sugarcane, maize, and sorghum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01226-z.
Collapse
Affiliation(s)
- Karoline Estefani Duarte
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of ABC, Santo André, SP 09210-580 Brazil
| | - Marcos Fernando Basso
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- BIOMOL/BIOTEC Laboratory, Mato Grosso Cotton Institute (IMAmt), Rondonópolis, MT 78740-970 Brazil
| | | | | | - Bruno de Oliveira Garcia
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of Lavras, Lavras, MG 37200-900 Brazil
| | | | | | | | | | - Thaís Ribeiro Santiago
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- University of Brasília, Brasília, DF 70910-900 Brazil
| | - Wagner Rodrigo de Souza
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of ABC, Santo André, SP 09210-580 Brazil
| | | |
Collapse
|
20
|
Li H, Li L, Wu W, Wang F, Zhou F, Lin Y. SvSTL1 in the large subunit family of ribonucleotide reductases plays a major role in chloroplast development of Setaria viridis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:625-641. [PMID: 35608125 DOI: 10.1111/tpj.15842] [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: 11/03/2021] [Revised: 05/04/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleotide reductases (RNRs) are essential enzymes in DNA synthesis. However, little is known about the RNRs in plants. Here, we identified a svstl1 mutant from the self-created ethyl methanesulfonate (EMS) mutant library of Setaria viridis. The mutant leaves exhibited a bleaching phenotype at the heading stage. Paraffin section analysis showed the destruction of the C4 Kranz anatomy. Transmission electron microscopy results further demonstrated the severely disturbed development of some chloroplasts. MutMap analysis revealed that the SvSTL1 gene is the primary candidate, encoding a large subunit of RNRs. Complementation experiments confirmed that SvSTL1 is responsible for the phenotype of svstl1. There are two additional RNR large subunit homologs in S. viridis, SvSTL2 and SvSTL3. To further understand the functions of these three RNR large subunit genes, a series of mutants were generated via CRISPR/Cas9 technology. In striking contrast to the finding that all three SvSTLs interact with the RNR small subunit, the phenotype varied along with the copies of chloroplast genome among different svstl single mutants: the svstl1 mutant exhibited pronounced chloroplast development and significantly fewer copies of the chloroplast genome than the svstl2 or svstl3 single mutants. These results suggested that SvSTL1 plays a major role in the optimal function of RNRs and is essential for chloroplast development. Furthermore, through the analysis of double and triple mutants, the study provides new insights into the finely tuned coordination among SvSTLs to maintain normal chloroplast development in the emerging C4 model plant S. viridis.
Collapse
Affiliation(s)
- Huanying Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Weichen Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
21
|
Toda E, Kiba T, Kato N, Okamoto T. Isolation of gametes and zygotes from Setaria viridis. JOURNAL OF PLANT RESEARCH 2022; 135:627-633. [PMID: 35534650 DOI: 10.1007/s10265-022-01393-w] [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: 02/20/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Setaria viridis, the wild ancestor of foxtail millet (Setaria italica), is an effective model plant for larger C4 crops because S. viridis has several desirable traits, such as short generation time, prolific seed production and a small genome size. These advantages are well suited for investigating molecular mechanisms in angiosperms, especially C4 crop species. Here, we report a procedure for isolating gametes and zygotes from S. viridis flowers. To isolate egg cells, ovaries were harvested from unpollinated mature flowers and cut transversely, which allowed direct access to the embryo sac. Thereafter, an egg cell was released from the cut end of the basal portion of the dissected ovary. To isolate sperm cells, pollen grains released from anthers were immersed in a mannitol solution, resulting in pollen-grain bursting, which released sperm cells. Additionally, S. viridis zygotes were successfully isolated from freshly pollinated flowers. Isolated zygotes cultured in a liquid medium developed into globular-like embryos and cell masses. Thus, isolated S. viridis gametes, zygotes and embryos are attainable for detailed observations and investigations of fertilization and developmental events in angiosperms.
Collapse
Affiliation(s)
- Erika Toda
- Plant Breeding Innovation Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0392, Japan.
- Department of Biological Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Takatoshi Kiba
- Plant Breeding Innovation Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Norio Kato
- Plant Breeding Innovation Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0392, Japan
| | - Takashi Okamoto
- Plant Breeding Innovation Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0392, Japan
| |
Collapse
|
22
|
Dangol A, Shavit R, Yaakov B, Strickler SR, Jander G, Tzin V. Characterizing serotonin biosynthesis in Setaria viridis leaves and its effect on aphids. PLANT MOLECULAR BIOLOGY 2022; 109:533-549. [PMID: 35020104 DOI: 10.1007/s11103-021-01239-4] [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: 07/08/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
A combined transcriptomic and metabolic analysis of Setaria viridis leaves responding to aphid infestation was used to identify genes related to serotonin biosynthesis. Setaria viridis (green foxtail), a short life-cycle C4 plant in the Poaceae family, is the wild ancestor of Setaria italica (foxtail millet), a resilient crop that provides good yields in dry and marginal land. Although S. viridis has been studied extensively in the last decade, the molecular mechanisms of insect resistance in this species remain under-investigated. To address this issue, we performed a metabolic analysis of S. viridis and discovered that these plants accumulate the tryptophan-derived compounds tryptamine and serotonin. To elucidate the defensive functions of serotonin, Rhophalosiphum padi (bird cherry-oat aphids) were exposed to this compound, either by exogenous application to the plant medium or with artificial diet bioassays. In both cases, exposure to serotonin increased aphid mortality. To identify genes that are involved in serotonin biosynthesis, we conducted a transcriptome analysis and identified several predicted S. viridis tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) genes. Two candidate genes were ectopically expressed in Nicotiana tabacum, where SvTDC1 (Sevir.6G066200) had tryptophan decarboxylase activity, and SvT5H1 (Sevir.8G219600) had tryptamine hydroxylase activity. Moreover, the function of the SvTDC1 gene was validated using virus-induced gene silencing in S. italica, which caused a reduction in serotonin levels. This study provides the first evidence of serotonin biosynthesis in Setaria leaves. The biosynthesis of serotonin may play an important role in defense responses and could prove to be useful for developing more pest-tolerant Setaria italica cultivars.
Collapse
Affiliation(s)
- Anuma Dangol
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | | | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
| |
Collapse
|
23
|
Read A, Weiss T, Crisp PA, Liang Z, Noshay J, Menard CC, Wang C, Song M, Hirsch CN, Springer NM, Zhang F. Genome-wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:103-116. [PMID: 35436373 PMCID: PMC9541237 DOI: 10.1111/tpj.15781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/12/2022] [Indexed: 05/17/2023]
Abstract
The DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs) are crucial for RNA-directed DNA methylation (RdDM) in plant species. Setaria viridis is a model monocot species with a relatively compact genome that has limited transposable element (TE) content. CRISPR-based genome editing approaches were used to create loss-of-function alleles for the two putative functional DRM genes in S. viridis to probe the role of RdDM. Double mutant (drm1ab) plants exhibit some morphological abnormalities but are fully viable. Whole-genome methylation profiling provided evidence for the widespread loss of methylation in CHH sequence contexts, particularly in regions with high CHH methylation in wild-type plants. Evidence was also found for the locus-specific loss of CG and CHG methylation, even in some regions that lack CHH methylation. Transcriptome profiling identified genes with altered expression in the drm1ab mutants. However, the majority of genes with high levels of CHH methylation directly surrounding the transcription start site or in nearby promoter regions in wild-type plants do not have altered expression in the drm1ab mutant, even when this methylation is lost, suggesting limited regulation of gene expression by RdDM. Detailed analysis of the expression of TEs identified several transposons that are transcriptionally activated in drm1ab mutants. These transposons are likely to require active RdDM for the maintenance of transcriptional repression.
Collapse
Affiliation(s)
- Andrew Read
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Trevor Weiss
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Peter A. Crisp
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
| | - Zhikai Liang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Jaclyn Noshay
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Claire C. Menard
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Chunfang Wang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Meredith Song
- Department of Genetics, Cell Biology and DevelopmentUniversity of MinnesotaMinneapolisMinnesota55108USA
| | - Candice N. Hirsch
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Nathan M. Springer
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Feng Zhang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| |
Collapse
|
24
|
Lai D, Fan Y, Xue G, He A, Yang H, He C, Li Y, Ruan J, Yan J, Cheng J. Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica). BMC Genomics 2022; 23:389. [PMID: 35596144 PMCID: PMC9122484 DOI: 10.1186/s12864-022-08633-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited. RESULTS: In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention. CONCLUSIONS In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet.
Collapse
Affiliation(s)
- Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
- School of Food and Biological Engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin He
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524000, People's Republic of China
| | - Yijing Li
- Henan Cancer Hospital, Zhengzhou, 450001, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Jun Yan
- School of Food and Biological Engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China.
| |
Collapse
|
25
|
Yi F, Huo M, Li J, Yu J. Time-series transcriptomics reveals a drought-responsive temporal network and crosstalk between drought stress and the circadian clock in foxtail millet. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1213-1228. [PMID: 35262997 DOI: 10.1111/tpj.15725] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Drought stress is a serious factor affecting crop growth and production worldwide. The circadian clock has been identified as key to improving regional adaptability of plants. However, our understanding of the contribution of the circadian clock to drought response and the impacts of drought stress on the circadian clock in plants is still limited. To explore the interactions between the circadian clock and drought stress, foxtail millet seedlings were treated with simulated drought (20% polyethylene glycol-6000) treatment starting at the day (DD) onset zeitgeber time 0 (ZT0, lights on) and at the night (DN) onset zeitgeber time 16 (ZT16, lights off). A high temporal-resolution transcriptomic investigation was performed using DD and DN samples collected at intervals of 2 or 4 h within a 24-h drought-treatment period. Overall, we identified 13 294 drought-responsive genes (DRGs). Among these DRGs, 7931 were common between DD and DN samples, 2638 were specific to DD, and 2725 were specific to DN. Additionally, we identified 1257 circadian genes, of which 67% were DRGs. Interestingly, with drought treatment starting at the day for 8, 12 or 16 h, the circadian phase shifted to 12 h. We also found that the circadian clock led to different day and night drought-responsive pathways. The identification of DRG_Clock (DRG and circadian clock) and DRG_NonClock (DRG and not circadian clock) genes provides a reference for selecting candidate drought resistance genes. Our work reveals the temporal drought-response process and crosstalk between drought stress and the circadian clock in foxtail millet.
Collapse
Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingyue Huo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianrui Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
26
|
Liu T, He J, Dong K, Wang X, Zhang L, Ren R, Huang S, Sun X, Pan W, Wang W, Yang P, Yang T, Zhang Z. Genome-wide identification of quantitative trait loci for morpho-agronomic and yield-related traits in foxtail millet (Setaria italica) across multi-environments. Mol Genet Genomics 2022; 297:873-888. [PMID: 35451683 PMCID: PMC9130181 DOI: 10.1007/s00438-022-01894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 03/31/2022] [Indexed: 11/21/2022]
Abstract
Foxtail millet (Setaria italica) is an ideal model of genetic system for functional genomics of the Panicoideae crop. Identification of QTL responsible for morpho-agronomic and yield-related traits facilitates dissection of genetic control and breeding in cereal crops. Here, based on a Yugu1 × Longgu7 RIL population and genome-wide resequencing data, an updated linkage map harboring 2297 bin and 74 SSR markers was constructed, spanning 1315.1 cM with an average distance of 0.56 cM between adjacent markers. A total of 221 QTL for 17 morpho-agronomic and yield-related traits explaining 5.5 ~ 36% of phenotypic variation were identified across multi-environments. Of these, 109 QTL were detected in two to nine environments, including the most stable qLMS6.1 harboring a promising candidate gene Seita.6G250500, of which 70 were repeatedly identified in different trials in the same geographic location, suggesting that foxtail millet has more identical genetic modules under the similar ecological environment. One hundred-thirty QTL with overlapping intervals formed 22 QTL clusters. Furthermore, six superior recombinant inbred lines, RIL35, RIL48, RIL77, RIL80, RIL115 and RIL125 with transgressive inheritance and enrichment of favorable alleles in plant height, tiller, panicle morphology and yield related-traits were screened by hierarchical cluster. These identified QTL, QTL clusters and superior lines lay ground for further gene-trait association studies and breeding practice in foxtail millet.
Collapse
Affiliation(s)
- Tianpeng Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Jihong He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Xuewen Wang
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, 30601, USA
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Sha Huang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Xiaoting Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wanxiang Pan
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wenwen Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Peng Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China.
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
| |
Collapse
|
27
|
Flexas J, Zhang Y, Gulías J, Xiong D, Carriquí M, Baraza E, Du T, Lei Z, Meng H, Dou H, Ribas-Carbo M, Xiang D, Xu W. Leaf physiological traits of plants from the Qinghai-Tibet Plateau and other arid sites in China: Identifying susceptible species and well-adapted extremophiles. JOURNAL OF PLANT PHYSIOLOGY 2022; 272:153689. [PMID: 35398716 DOI: 10.1016/j.jplph.2022.153689] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Extreme environments, such as deserts and high-elevation ecosystems, are very important from biodiversity and ecological perspectives. However, plant physiology at those sites has been scarcely studied, likely due to logistic difficulties. In the present study, leaf physiological traits in native plants were analyzed from arid zones across an elevational transect in Western China, from Turpan Basin to the Qinghai-Tibet Plateau (QTP) at Delingha. The aim of this study was to use leaf physiological traits to help identifying potentially threatened species and true extremophiles. Physiological measurements in the field, and particularly in situ measurements of gas exchange and chlorophyll fluorescence, have been determined to be useful to determine the current state of plants at a given environment. Using this approach plus a combination of leaf traits, several species performing particularly well at the QTP were identified, e.g. Hedysarum multijugum, as well as at Manas drylands, e.g. Peganum harmala and Setaria viridis. On the other hand, several species showed marked signs of severe stress, in particular a very low photosynthetic rate over its potential maximum, as well as other negative traits, like low water and/or nitrogen-use-efficiency, which should be considered in conservation plans. Interestingly, all C4 species studied except Setaria viridis were among the most stressed species. Despite their higher water use efficiency and drought-tolerance reputation, they presented a much larger photosynthesis depression than most C3 species. This is an intriguing and interesting observation that deserves further studies.
Collapse
Affiliation(s)
- Jaume Flexas
- Research Group on Plant Biology Under Mediterranean Conditions, Department de Biologia, Universitat de Les Illes Balears (UIB) - Agro-Environmental and Water Economics Institute (INAGEA), Carretera de Valldemossa Km 7.5, 07122, Palma, Illes Balears, Spain; King Abdulaziz University, P.O. Box 80200, Jeddah, 21589, Saudi Arabia.
| | - Yali Zhang
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps / College of Agriculture/College of Life Science, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Javier Gulías
- Research Group on Plant Biology Under Mediterranean Conditions, Department de Biologia, Universitat de Les Illes Balears (UIB) - Agro-Environmental and Water Economics Institute (INAGEA), Carretera de Valldemossa Km 7.5, 07122, Palma, Illes Balears, Spain
| | - Dongliang Xiong
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marc Carriquí
- Research Group on Plant Biology Under Mediterranean Conditions, Department de Biologia, Universitat de Les Illes Balears (UIB) - Agro-Environmental and Water Economics Institute (INAGEA), Carretera de Valldemossa Km 7.5, 07122, Palma, Illes Balears, Spain
| | - Elena Baraza
- Research Group on Plant Biology Under Mediterranean Conditions, Department de Biologia, Universitat de Les Illes Balears (UIB) - Agro-Environmental and Water Economics Institute (INAGEA), Carretera de Valldemossa Km 7.5, 07122, Palma, Illes Balears, Spain
| | - Tingting Du
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhangying Lei
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps / College of Agriculture/College of Life Science, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Haofeng Meng
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps / College of Agriculture/College of Life Science, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Haitao Dou
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps / College of Agriculture/College of Life Science, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Miquel Ribas-Carbo
- Research Group on Plant Biology Under Mediterranean Conditions, Department de Biologia, Universitat de Les Illes Balears (UIB) - Agro-Environmental and Water Economics Institute (INAGEA), Carretera de Valldemossa Km 7.5, 07122, Palma, Illes Balears, Spain
| | - Dao Xiang
- Wulanwusu Agro-Meteorological Experiment Station of Xinjiang / Wulanwusu National Comprehensive Meteorological Observation Special Test Field, Wulanwusu, 832199, Xinjiang, China
| | - Wenbin Xu
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps / College of Agriculture/College of Life Science, Shihezi University, Shihezi, Xinjiang, 832003, China
| |
Collapse
|
28
|
Shamseldin A. Future Outlook of Transferring Biological Nitrogen Fixation (BNF) to Cereals and Challenges to Retard Achieving this Dream. Curr Microbiol 2022; 79:171. [PMID: 35476236 DOI: 10.1007/s00284-022-02852-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 03/21/2022] [Indexed: 11/03/2022]
Abstract
BNF is a fascinating phenomenon which contributes to protect the nature from environmental pollution that can be happened as a result of heavy nitrogen applications. The importance of BNF is due to its supply of the agricultural lands with about 200 million tons of N annually. In this biological process, a specific group of bacteria collectively called rhizobia fix the atmospheric N in symbiosis with legumes called symbiotic nitrogen fixation and others (free living) fix nitrogen gas from the atmosphere termed asymbiotic. Several trials were done by scientists around the world to make cereals more benefited from nitrogen gas through different approaches. The first approach is to engineer cereals to form nodulated roots. Secondly is to transfer nif genes directly to cereals and fix N without Rhizobium partner. The other two approaches are maximizing the inoculation of cereals with both of diazotrophs or endophytes. Recently, scientists solved some challenges that entangle engineering cereals with nif genes directly and they confirmed the suitability of mitochondria and plastids as a suitable place for better biological function of nif genes expression in cereals. Fortunately, this article is confirming the success of scientists not only to transfer synthetic nitrogenase enzyme to Escherichia coli that gave 50% of its activity of expression, but also move it to plants as Nicotiana benthamiana. This mini review aims at explaining the future outlook of BNF and the challenges limiting its transfer to cereals and levels of success to make cereals self nitrogen fixing.
Collapse
Affiliation(s)
- Abdelaal Shamseldin
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria, Egypt.
| |
Collapse
|
29
|
Tang S, Shahriari M, Xiang J, Pasternak T, Igolkina A, Aminizade S, Zhi H, Gao Y, Roodbarkelari F, Sui Y, Jia G, Wu C, Zhang L, Zhao L, Li X, Meshcheryakov G, Samsonova M, Diao X, Palme K, Teale W. The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2021-2034. [PMID: 34940828 DOI: 10.1093/jxb/erab556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from Rubisco. The specialized leaf anatomy required for this separation evolved independently many times. The morphology of C4 root systems is also distinctive and adapted to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture. Using a mutant screen in the C4 model plant Setaria italica, we identify Siaux1-1 and Siaux1-2 as root system architecture mutants. Unlike in S. viridis, AUX1 promotes lateral root development in S. italica. A cell by cell analysis of the Siaux1-1 root apical meristem revealed changes in the distribution of cell volumes in all cell layers and a dependence of the frequency of protophloem and protoxylem strands on SiAUX1. We explore the molecular basis of the role of SiAUX1 in seedling development using an RNAseq analysis of wild-type and Siaux1-1 plants and present novel targets for SiAUX1-dependent gene regulation. Using a selection sweep and haplotype analysis of SiAUX1, we show that Hap-2412TT in the promoter region of SiAUX1 is an allele which is associated with lateral root number and has been strongly selected for during Setaria domestication.
Collapse
Affiliation(s)
- Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mojgan Shahriari
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Jishan Xiang
- Academy of Agricultural Sciences/Key Laboratory of Regional Ecological Protection & Agricultural and Animal Husbandry Development, Chifeng University, Chifeng, 024000, Inner Mongolia, China
| | - Taras Pasternak
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Anna Igolkina
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnic University, St. Petersburg, 195259, Russia
| | | | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanzhu Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Farshad Roodbarkelari
- Institute of Biology III, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Linlin Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xugang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Georgy Meshcheryakov
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnic University, St. Petersburg, 195259, Russia
| | - Maria Samsonova
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnic University, St. Petersburg, 195259, Russia
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Klaus Palme
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
- Centre of Biological Systems Analysis and BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - William Teale
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| |
Collapse
|
30
|
Li J, Zhang L, G. Elbaiomy R, Chen L, Wang Z, Jiao J, Zhu J, Zhou W, Chen B, Soaud SA, Abbas M, Lin N, El-Sappah AH. Evolution analysis of FRIZZY PANICLE ( FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae). PeerJ 2022; 10:e12880. [PMID: 35295554 PMCID: PMC8919851 DOI: 10.7717/peerj.12880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
FRIZZY PANICLE (FZP), an essential gene that controls spikelet differentiation and development in the grass family (Poaceae), prevents the formation of axillary bud meristems and is closely associated with crop yields. It is unclear whether the FZP gene or its orthologs were selected during the evolutionary process of grass species, which possess diverse spike morphologies. In the present study, we adopted bioinformatics methods for the evolutionary analysis of FZP orthologs in species of the grass family. Thirty-five orthologs with protein sequences identical to that of the FZP gene were identified from 29 grass species. Analysis of conserved domains revealed that the AP2/ERF domains were highly conserved with almost no amino acid mutations. However, species of the tribe Triticeae, genus Oryza, and C4 plants exhibited more significant amino acid mutations in the acidic C-terminus region. Results of the phylogenetic analysis showed that the 29 grass species could be classified into three groups, namely, Triticeae, Oryza, and C4 plants. Within the Triticeae group, the FZP genes originating from the same genome were classified into the same sub-group. When selection pressure analysis was performed, significant positive selection sites were detected in species of the Triticeae and Oryza groups. Our results show that the FZP gene was selected during the grass family's evolutionary process, and functional divergence may have already occurred among the various species. Therefore, researchers investigating the FZP gene's functions should take note of the possible presence of various roles in other grass species.
Collapse
Affiliation(s)
- Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Litian Zhang
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | | | - Lilan Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Zhenrong Wang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jie Jiao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jiliang Zhu
- Agriculture and Rural Bureau of Zhongjiang County, Deyang, Sichuan, China
| | - Wanhai Zhou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Bo Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Na Lin
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| |
Collapse
|
31
|
Role of Cytosolic Malic Enzyme in Oleaginicity of High-Lipid-Producing Fungal Strain Mucor circinelloides WJ11. J Fungi (Basel) 2022; 8:jof8030265. [PMID: 35330267 PMCID: PMC8955760 DOI: 10.3390/jof8030265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Abstract
Mucor circinelloides, an oleaginous filamentous fungus, is gaining popularity due to its ability to synthesize significant amounts of lipids containing γ-linolenic acid (GLA) that have important health benefits. Malic enzyme (ME), which serves as the main source of NADPH in some fungi, has been found to regulate lipid accumulation in oleaginous fungi. In the present study, the role of two cytosolic ME genes, cmalA and cmalB, in the lipid accumulation of the M. circinelloides high-lipid-producing strain WJ11, was evaluated. Strains overexpressing cmalA and cmalB showed a 9.8- and 6.4-fold rise in specific ME activity, respectively, and an elevation of the lipid content by 23.2% and 5.8%, respectively, suggesting that these genes are involved in lipid biosynthesis. Due to increased lipid accumulation, overall GLA content in biomass was observed to be elevated by 11.42% and 16.85% in cmalA and cmalB overexpressing strains, respectively. Our study gives an important insight into different studies exploring the role of the cmalA gene, while we have for the first time investigated the role of the cmalB gene in the M. circinelloides WJ11 strain.
Collapse
|
32
|
Ajeesh Krishna TP, Maharajan T, Ceasar SA. Improvement of millets in the post-genomic era. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:669-685. [PMID: 35465206 PMCID: PMC8986959 DOI: 10.1007/s12298-022-01158-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 05/16/2023]
Abstract
Millets are food and nutrient security crops in the semi-arid tropics of developing countries. Crop improvement using modern tools is one of the priority areas of research in millets. The whole-genome sequence (WGS) of millets provides new insight into understanding and studying the genes, genome organization and genomic-assisted improvement of millets. The WGS of millets helps to carry out genome-wide comparison and co-linearity studies among millets and other cereal crops. This approach might lead to the identification of genes underlying biotic and abiotic stress tolerance in millets. The available genome sequence of millets can be used for SNP identification, allele discovery, association and linkage mapping, identification of valuable candidate genes, and marker-assisted breeding (MAB) programs. Next generation sequencing (NGS) technology provides opportunities for genome-assisted breeding (GAB) through genomic selection (GS) and genome-wide association studies (GAWS) for crop improvement. Clustered, regularly interspaced, short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) genome editing (GE) system provides new opportunities for millet improvement. In this review, we discuss the details on the WGS available for millets and highlight the importance of utilizing such resources in the post-genomic era for millet improvement. We also draw inroads on the utilization of various approaches such as GS, GWAS, functional genomics, gene validation and GE for millet improvement. This review might be helpful for understanding the developments in the post-genomic era of millet improvement.
Collapse
Affiliation(s)
- T P Ajeesh Krishna
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| | - T Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| | - S Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| |
Collapse
|
33
|
Peterson MJ, Handakumbura PP, Thompson AM, Russell ZR, Kim YM, Fansler SJ, Smith ML, Toyoda JG, Chu RK, Stanfill BA, Fransen SC, Bailey VL, Jansson C, Hixson KK, Callister SJ. Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil. PLoS One 2021; 16:e0259937. [PMID: 34879068 PMCID: PMC8654227 DOI: 10.1371/journal.pone.0259937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
The microbial and molecular characterization of the ectorhizosphere is an important step towards developing a more complete understanding of how the cultivation of biofuel crops can be undertaken in nutrient poor environments. The ectorhizosphere of Setaria is of particular interest because the plant component of this plant-microbe system is an important agricultural grain crop and a model for biofuel grasses. Importantly, Setaria lends itself to high throughput molecular studies. As such, we have identified important intra- and interspecific microbial and molecular differences in the ectorhizospheres of three geographically distant Setaria italica accessions and their wild ancestor S. viridis. All were grown in a nutrient-poor soil with and without nutrient addition. To assess the contrasting impact of nutrient deficiency observed for two S. italica accessions, we quantitatively evaluated differences in soil organic matter, microbial community, and metabolite profiles. Together, these measurements suggest that rhizosphere priming differs with Setaria accession, which comes from alterations in microbial community abundances, specifically Actinobacteria and Proteobacteria populations. When globally comparing the metabolomic response of Setaria to nutrient addition, plants produced distinctly different metabolic profiles in the leaves and roots. With nutrient addition, increases of nitrogen containing metabolites were significantly higher in plant leaves and roots along with significant increases in tyrosine derived alkaloids, serotonin, and synephrine. Glycerol was also found to be significantly increased in the leaves as well as the ectorhizosphere. These differences provide insight into how C4 grasses adapt to changing nutrient availability in soils or with contrasting fertilization schemas. Gained knowledge could then be utilized in plant enhancement and bioengineering efforts to produce plants with superior traits when grown in nutrient poor soils.
Collapse
Affiliation(s)
- Matthew J. Peterson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Pubudu P. Handakumbura
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Allison M. Thompson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Zachary R. Russell
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Sarah J. Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Montana L. Smith
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Jason G. Toyoda
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Rosey K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Bryan A. Stanfill
- Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Steven C. Fransen
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington, United States of America
| | - Vanessa L. Bailey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (SJC); (KKH)
| | - Stephen J. Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (SJC); (KKH)
| |
Collapse
|
34
|
Ortiz-Ramírez C, Guillotin B, Xu X, Rahni R, Zhang S, Yan Z, Coqueiro Dias Araujo P, Demesa-Arevalo E, Lee L, Van Eck J, Gingeras TR, Jackson D, Gallagher KL, Birnbaum KD. Ground tissue circuitry regulates organ complexity in maize and Setaria. Science 2021; 374:1247-1252. [PMID: 34855479 DOI: 10.1126/science.abj2327] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Carlos Ortiz-Ramírez
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.,UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato 36821, México
| | - Bruno Guillotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ramin Rahni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Sanqiang Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Zhe Yan
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 1904, USA
| | | | | | - Laura Lee
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kimberly L Gallagher
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 1904, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| |
Collapse
|
35
|
Travassos-Lins J, de Oliveira Rocha CC, de Souza Rodrigues T, Alves-Ferreira M. Evaluation of the molecular and physiological response to dehydration of two accessions of the model plant Setaria viridis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:211-223. [PMID: 34808464 DOI: 10.1016/j.plaphy.2021.11.015] [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: 10/13/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Water deficits are responsible for countless agricultural losses. Among the affected crops, C4 plants are of special interest due to their high water and nitrogen use efficiency. Two accessions of Setaria viridis (Ast-1 and A10.1) with contrasting responses to water deficit were used in the current work to better understand the mechanisms behind drought tolerance in C4 species. Our results showed that although the A10.1 accession exhibited a reduced size and lower Rfd values in comparison to Ast-1, it had overall higher Fv/Fm and lower NPQ values in well-watered conditions. The water deficit induction was performed with PEG-8000 at the grain-filling stage using dehydration cycles. Analysis of physiological measurements showed the A10.1 accession as being more tolerant to multiple water deficit exposures. In addition, PCA identified a clear difference in the pattern of drought response of the accessions. Four drought marker genes previously described in the literature were chosen to evaluate the response at the molecular level: SvP5CS2, SvDHN1, SvNAC6, and SvWRKY1. Besides confirming that Ast-1 is a more sensitive accession, the expression analysis revealed that SvNAC1 might better monitor drought stress, while SvWRKY1 was able to differentiate the two accessions. Distinct evolutionary histories of each accession may be behind their differences in response to water deficits.
Collapse
Affiliation(s)
- João Travassos-Lins
- Laboratory of Plant Molecular Genetics and Biotechnology, Federal University of Rio de Janeiro, Biology Institute, Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Caio César de Oliveira Rocha
- Laboratory of Plant Molecular Genetics and Biotechnology, Federal University of Rio de Janeiro, Biology Institute, Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Tamires de Souza Rodrigues
- Laboratory of Plant Molecular Genetics and Biotechnology, Federal University of Rio de Janeiro, Biology Institute, Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Marcio Alves-Ferreira
- Laboratory of Plant Molecular Genetics and Biotechnology, Federal University of Rio de Janeiro, Biology Institute, Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil.
| |
Collapse
|
36
|
Ermakova M, Osborn H, Groszmann M, Bala S, Bowerman A, McGaughey S, Byrt C, Alonso-Cantabrana H, Tyerman S, Furbank RT, Sharwood RE, von Caemmerer S. Expression of a CO 2-permeable aquaporin enhances mesophyll conductance in the C 4 species Setaria viridis. eLife 2021; 10:70095. [PMID: 34842138 PMCID: PMC8648302 DOI: 10.7554/elife.70095] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/23/2021] [Indexed: 02/02/2023] Open
Abstract
A fundamental limitation of photosynthetic carbon fixation is the availability of CO2. In C4 plants, primary carboxylation occurs in mesophyll cytosol, and little is known about the role of CO2 diffusion in facilitating C4 photosynthesis. We have examined the expression, localization, and functional role of selected plasma membrane intrinsic aquaporins (PIPs) from Setaria italica (foxtail millet) and discovered that SiPIP2;7 is CO2-permeable. When ectopically expressed in mesophyll cells of Setaria viridis (green foxtail), SiPIP2;7 was localized to the plasma membrane and caused no marked changes in leaf biochemistry. Gas exchange and C18O16O discrimination measurements revealed that targeted expression of SiPIP2;7 enhanced the conductance to CO2 diffusion from the intercellular airspace to the mesophyll cytosol. Our results demonstrate that mesophyll conductance limits C4 photosynthesis at low pCO2 and that SiPIP2;7 is a functional CO2 permeable aquaporin that can improve CO2 diffusion at the airspace/mesophyll interface and enhance C4 photosynthesis.
Collapse
Affiliation(s)
- Maria Ermakova
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Hannah Osborn
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Michael Groszmann
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Soumi Bala
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Andrew Bowerman
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Samantha McGaughey
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Caitlin Byrt
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Hugo Alonso-Cantabrana
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Steve Tyerman
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture Food and Wine, University of Adelaide, Adelaide, Australia
| | - Robert T Furbank
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Robert E Sharwood
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia
| | - Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| |
Collapse
|
37
|
Cui H. Challenges and Approaches to Crop Improvement Through C3-to-C4 Engineering. FRONTIERS IN PLANT SCIENCE 2021; 12:715391. [PMID: 34594351 PMCID: PMC8476962 DOI: 10.3389/fpls.2021.715391] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/06/2021] [Indexed: 05/24/2023]
Abstract
With a rapidly growing world population and dwindling natural resources, we are now facing the enormous challenge of increasing crop yields while simultaneously improving the efficiency of resource utilization. Introduction of C4 photosynthesis into C3 crops is widely accepted as a key strategy to meet this challenge because C4 plants are more efficient than C3 plants in photosynthesis and resource usage, particularly in hot climates, where the potential for productivity is high. Lending support to the feasibility of this C3-to-C4 engineering, evidence indicates that C4 photosynthesis has evolved from C3 photosynthesis in multiple lineages. Nevertheless, C3-to-C4 engineering is not an easy task, as several features essential to C4 photosynthesis must be introduced into C3 plants. One such feature is the spatial separation of the two phases of photosynthesis (CO2 fixation and carbohydrate synthesis) into the mesophyll and bundle sheath cells, respectively. Another feature is the Kranz anatomy, characterized by a close association between the mesophyll and bundle sheath (BS) cells (1:1 ratio). These anatomical features, along with a C4-specific carbon fixation enzyme (PEPC), form a CO2-concentration mechanism that ensures a high photosynthetic efficiency. Much effort has been taken in the past to introduce the C4 mechanism into C3 plants, but none of these attempts has met with success, which is in my opinion due to a lack of system-level understanding and manipulation of the C3 and C4 pathways. As a prerequisite for the C3-to-C4 engineering, I propose that not only the mechanisms that control the Kranz anatomy and cell-type-specific expression in C3 and C4 plants must be elucidated, but also a good understanding of the gene regulatory network underlying C3 and C4 photosynthesis must be achieved. In this review, I first describe the past and current efforts to increase photosynthetic efficiency in C3 plants and their limitations; I then discuss a systems approach to tackling down this challenge, some practical issues, and recent technical innovations that would help us to solve these problems.
Collapse
Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
- College of Life Science, Northwest Science University of Agriculture and Forestry, Yangling, China
| |
Collapse
|
38
|
von Caemmerer S. Updating the steady-state model of C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6003-6017. [PMID: 34173821 PMCID: PMC8411607 DOI: 10.1093/jxb/erab266] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 05/22/2023]
Abstract
C4 plants play a key role in world agriculture. For example, C4 crops such as maize and sorghum are major contributors to food production in both developed and developing countries, and the C4 grasses sugarcane, miscanthus, and switchgrass are major plant sources of bioenergy. In the challenge to manipulate and enhance C4 photosynthesis, steady-state models of leaf photosynthesis provide an important tool for gas exchange analysis and thought experiments that can explore photosynthetic pathway changes. Here a previous C4 photosynthetic model developed by von Caemmerer and Furbank has been updated with new kinetic parameterization and temperature dependencies added. The parameterization was derived from experiments on the C4 monocot, Setaria viridis, which for the first time provides a cohesive parameterization. Mesophyll conductance and its temperature dependence have also been included, as this is an important step in the quantitative correlation between the initial slope of the CO2 response curve of CO2 assimilation and in vitro phosphoenolpyruvate carboxylase activity. Furthermore, the equations for chloroplast electron transport have been updated to include cyclic electron transport flow, and equations have been added to calculate the electron transport rate from measured CO2 assimilation rates.
Collapse
Affiliation(s)
- Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
- Correspondence:
| |
Collapse
|
39
|
von Caemmerer S. Updating the steady-state model of C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021. [PMID: 34173821 DOI: 10.5061/dryad.zcrjdfnc3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
C4 plants play a key role in world agriculture. For example, C4 crops such as maize and sorghum are major contributors to food production in both developed and developing countries, and the C4 grasses sugarcane, miscanthus, and switchgrass are major plant sources of bioenergy. In the challenge to manipulate and enhance C4 photosynthesis, steady-state models of leaf photosynthesis provide an important tool for gas exchange analysis and thought experiments that can explore photosynthetic pathway changes. Here a previous C4 photosynthetic model developed by von Caemmerer and Furbank has been updated with new kinetic parameterization and temperature dependencies added. The parameterization was derived from experiments on the C4 monocot, Setaria viridis, which for the first time provides a cohesive parameterization. Mesophyll conductance and its temperature dependence have also been included, as this is an important step in the quantitative correlation between the initial slope of the CO2 response curve of CO2 assimilation and in vitro phosphoenolpyruvate carboxylase activity. Furthermore, the equations for chloroplast electron transport have been updated to include cyclic electron transport flow, and equations have been added to calculate the electron transport rate from measured CO2 assimilation rates.
Collapse
Affiliation(s)
- Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| |
Collapse
|
40
|
Huangfu Y, Pan J, Li Z, Wang Q, Mastouri F, Li Y, Yang S, Liu M, Dai S, Liu W. Genome-wide identification of PTI1 family in Setaria italica and salinity-responsive functional analysis of SiPTI1-5. BMC PLANT BIOLOGY 2021; 21:319. [PMID: 34217205 PMCID: PMC8254068 DOI: 10.1186/s12870-021-03077-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/27/2021] [Indexed: 05/18/2023]
Abstract
BACKGROUND PTI1 (Pto-interacting 1) protein kinase belongs to the receptor-like cytoplasmic kinase (RLCK) group of receptor-like protein kinases (RLK), but lack extracellular and transmembrane domains. PTI1 was first identified in tomato (Solanum lycopersicum) and named SlPTI1, which has been reported to interact with bacterial effector Pto, a serine/threonine protein kinase involved in plant resistance to bacterial disease. Briefly, the host PTI1 specifically recognizes and interacts with the bacterial effector AvrPto, which triggers hypersensitive cell death to inhibit the pathogen growth in the local infection site. Previous studies have demonstrated that PTI1 is associated with oxidative stress and hypersensitivity. RESULTS We identified 12 putative PTI1 genes from the genome of foxtail millet (Setaria italica) in this study. Gene replication analysis indicated that both segmental replication events played an important role in the expansion of PTI1 gene family in foxtail millet. The PTI1 family members of model plants, i.e. S. italica, Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), maize (Zea mays), S. lycopersicum, and soybean (Glycine max), were classified into six major categories according to the phylogenetic analysis, among which the PTI1 family members in foxtail millet showed higher degree of homology with those of rice and maize. The analysis of a complete set of SiPTI1 genes/proteins including classification, chromosomal location, orthologous relationships and duplication. The tissue expression characteristics revealed that SiPTI1 genes are mainly expressed in stems and leaves. Experimental qRT-PCR results demonstrated that 12 SiPTI1 genes were induced by multiple stresses. Subcellular localization visualized that all of foxtail millet SiPTI1s were localized to the plasma membrane. Additionally, heterologous expression of SiPTI1-5 in yeast and E. coli enhanced their tolerance to salt stress. CONCLUSIONS Our results contribute to a more comprehensive understanding of the roles of PTI1 protein kinases and will be useful in prioritizing particular PTI1 for future functional validation studies in foxtail millet.
Collapse
Affiliation(s)
- Yongguan Huangfu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Jiaowen Pan
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Zhen Li
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Qingguo Wang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Fatemeh Mastouri
- Bota Bioscience, 325 Vassar st. Suite 2a, Cambridge, MA, 02139, USA
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Stephen Yang
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr, Rockville, MD, 20850, USA
| | - Min Liu
- Shandong Agriculture and Engineering University, Jinan, 250100, Shandong, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Wei Liu
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, China.
| |
Collapse
|
41
|
Ribeiro AP, Vinecky F, Duarte KE, Santiago TR, das Chagas Noqueli Casari RA, Hell AF, da Cunha BADB, Martins PK, da Cruz Centeno D, de Oliveira Molinari PA, de Almeida Cançado GM, Magalhães JVD, Kobayashi AK, de Souza WR, Molinari HBC. Enhanced aluminum tolerance in sugarcane: evaluation of SbMATE overexpression and genome-wide identification of ALMTs in Saccharum spp. BMC PLANT BIOLOGY 2021; 21:300. [PMID: 34187360 PMCID: PMC8240408 DOI: 10.1186/s12870-021-02975-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/14/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND A major limiting factor for plant growth is the aluminum (Al) toxicity in acidic soils, especially in tropical regions. The exclusion of Al from the root apex through root exudation of organic acids such as malate and citrate is one of the most ubiquitous tolerance mechanisms in the plant kingdom. Two families of anion channels that confer Al tolerance are well described in the literature, ALMT and MATE family. RESULTS In this study, sugarcane plants constitutively overexpressing the Sorghum bicolor MATE gene (SbMATE) showed improved tolerance to Al when compared to non-transgenic (NT) plants, characterized by sustained root growth and exclusion of aluminum from the root apex based on the result obtained with hematoxylin staining. In addition, genome-wide analysis of the recently released sugarcane genome identified 11 ALMT genes and molecular studies showed potential new targets for aluminum tolerance. CONCLUSIONS Our results indicate that the transgenic plants overexpressing the Sorghum bicolor MATE has an improved tolerance to Al. The expression profile of ALMT genes revels potential candidate genes to be used has an alternative for agricultural expansion in Brazil and other areas with aluminum toxicity in poor and acid soils.
Collapse
Affiliation(s)
- Ana Paula Ribeiro
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasilia, 70770-901, DF, Brazil
| | - Felipe Vinecky
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasilia, 70770-901, DF, Brazil
| | - Karoline Estefani Duarte
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasilia, 70770-901, DF, Brazil
- Centre of Natural Sciences and Humanities, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil
| | - Thaís Ribeiro Santiago
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasilia, 70770-901, DF, Brazil
- Phytopathology Department, University of Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | | | - Aline Forgatti Hell
- Centre of Natural Sciences and Humanities, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil
| | | | - Polyana Kelly Martins
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasilia, 70770-901, DF, Brazil
| | - Danilo da Cruz Centeno
- Centre of Natural Sciences and Humanities, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil
| | | | | | | | | | - Wagner Rodrigo de Souza
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasilia, 70770-901, DF, Brazil.
- Centre of Natural Sciences and Humanities, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil.
| | | |
Collapse
|
42
|
Schnabel T, Sattely E. Engineering Posttranslational Regulation of Glutamine Synthetase for Controllable Ammonia Production in the Plant Symbiont Azospirillum brasilense. Appl Environ Microbiol 2021; 87:e0058221. [PMID: 33962983 PMCID: PMC8231714 DOI: 10.1128/aem.00582-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/27/2021] [Indexed: 11/20/2022] Open
Abstract
Nitrogen requirements for modern agriculture far exceed the levels of bioavailable nitrogen in most arable soils. As a result, the addition of nitrogen fertilizer is necessary to sustain productivity and yields, especially for cereal crops, the planet's major calorie suppliers. Given the unsustainability of industrial fertilizer production and application, engineering biological nitrogen fixation directly at the roots of plants has been a grand challenge for biotechnology. Here, we designed and tested a potentially broadly applicable metabolic engineering strategy for the overproduction of ammonia in the diazotrophic symbiont Azospirillum brasilense. Our approach is based on an engineered unidirectional adenylyltransferase (uAT) that posttranslationally modifies and deactivates glutamine synthetase (GS), a key regulator of nitrogen metabolism in the cell. We show that this circuit can be controlled inducibly, and we leveraged the inherent self-contained nature of our posttranslational approach to demonstrate that multicopy redundancy can improve strain evolutionary stability. uAT-engineered Azospirillum is capable of producing ammonia at rates of up to 500 μM h-1 unit of OD600 (optical density at 600 nm)-1. We demonstrated that when grown in coculture with the model monocot Setaria viridis, these strains increase the biomass and chlorophyll content of plants up to 54% and 71%, respectively, relative to the wild type (WT). Furthermore, we rigorously demonstrated direct transfer of atmospheric nitrogen to extracellular ammonia and then plant biomass using isotopic labeling: after 14 days of cocultivation with engineered uAT strains, 9% of chlorophyll nitrogen in Setaria seedlings was derived from diazotrophically fixed dinitrogen, whereas no nitrogen was incorporated in plants cocultivated with WT controls. This rational design for tunable ammonia overproduction is modular and flexible, and we envision that it could be deployable in a consortium of nitrogen-fixing symbiotic diazotrophs for plant fertilization. IMPORTANCE Nitrogen is the most limiting nutrient in modern agriculture. Free-living diazotrophs, such as Azospirillum, are common colonizers of cereal grasses and have the ability to fix nitrogen but natively do not release excess ammonia. Here, we used a rational engineering approach to generate ammonia-excreting strains of Azospirillum. Our design features posttranslational control of highly conserved central metabolism, enabling tunability and flexibility of circuit placement. We found that our strains promote the growth and health of the model grass S. viridis and rigorously demonstrated that in comparison to WT controls, our engineered strains can transfer nitrogen from 15N2 gas to plant biomass. Unlike previously reported ammonia-producing mutants, our rationally designed approach easily lends itself to further engineering opportunities and has the potential to be broadly deployable.
Collapse
Affiliation(s)
- Tim Schnabel
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University and HHMI, Stanford, California, USA
| |
Collapse
|
43
|
Basso MF, Duarte KE, Santiago TR, de Souza WR, Garcia BDO, da Cunha BDB, Kobayashi AK, Molinari HBC. Efficient genome editing and gene knockout in Setaria viridis with CRISPR/Cas9 directed gene editing by the non-homologous end-joining pathway. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:227-238. [PMID: 34393601 PMCID: PMC8329270 DOI: 10.5511/plantbiotechnology.21.0407a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/07/2021] [Indexed: 05/05/2023]
Abstract
The CRISPR/Cas9 system has been used for genome editing in several organisms, including higher plants. This system induces site-specific mutations in the genome based on the nucleotide sequence of engineered guide RNAs. The complex genomes of C4 grasses makes genome editing a challenge in key grass crops like maize (Zea mays), sorghum (Sorghum bicolor), Brachiaria spp., switchgrass (Panicum virgatum), and sugarcane (Saccharum spp.). Setaria viridis is a diploid C4 grass widely used as a model for these C4 crop plants. Here, an optimized CRISPR/Cas9 binary vector that exploits the non-homologous end joining (NHEJ) system was used to knockout a green fluorescent protein (gfp) transgene in S. viridis accession A10.1. Transformation of embryogenic callus by A. tumefaciens generated ten glufosinate-ammonium resistant transgenic events. In the T0 generation, 60% of the events were biallelic mutants in the gfp transgene with no detectable accumulation of GFP protein and without insertions or deletions in predicted off-target sites. The gfp mutations generated by CRISPR/Cas9 were stable and displayed Mendelian segregation in the T1 generation. Altogether, the system described here is a highly efficient genome editing system for S. viridis, an important model plant for functional genomics studies in C4 grasses. Also, this system is a potential tool for improvement of agronomic traits in C4 crop plants with complex genomes.
Collapse
Affiliation(s)
- Marcos Fernando Basso
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- BIOMOL/BIOTEC Laboratory, Mato Grosso Cotton Institute (IMAmt), Rondonópolis, MT, 78740-970, Brazil
| | - Karoline Estefani Duarte
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- Center for Natural and Human Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, São Paulo, 09606-045, Brazil
| | - Thais Ribeiro Santiago
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- Departament of Phytopathology, Federal University of Brasília, Brasília (UNB), Distrito Federal, 70910-900, Brazil
| | - Wagner Rodrigo de Souza
- Center for Natural and Human Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, São Paulo, 09606-045, Brazil
| | - Bruno de Oliveira Garcia
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Bárbara Dias Brito da Cunha
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Adilson Kenji Kobayashi
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Hugo Bruno Correa Molinari
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- E-mail: Tel: +55-61-3448-2307, Fax: +55-61-34481598
| |
Collapse
|
44
|
Prakash PT, Banan D, Paul RE, Feldman MJ, Xie D, Freyfogle L, Baxter I, Leakey ADB. Correlation and co-localization of QTL for stomatal density, canopy temperature, and productivity with and without drought stress in Setaria. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5024-5037. [PMID: 33893796 PMCID: PMC8219040 DOI: 10.1093/jxb/erab166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/23/2021] [Indexed: 05/04/2023]
Abstract
Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C4 genus, Setaria. Recombinant inbred lines (RILs) derived from a Setaria italica×Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning, and canopy temperature was measured using infrared imaging. Stomatal density and canopy temperature were positively correlated but both were negatively correlated with total above-ground biomass. These trait relationships suggest a likely interaction between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple quantitative trait loci (QTL) were identified for stomatal density and canopy temperature, including co-located QTL on chromosomes 5 and 9. The direction of the additive effect of these QTL on chromosome 5 and 9 was in accordance with the positive phenotypic relationship between these two traits. This, along with prior experiments, suggests a common genetic architecture between stomatal patterning and WUE in controlled environments with canopy transpiration and productivity in the field, while highlighting the potential of Setaria as a model to understand the physiology and genetics of WUE in C4 species.
Collapse
Affiliation(s)
- Parthiban Thathapalli Prakash
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- International Rice Research Institute, Los Baños, Philippines
| | - Darshi Banan
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rachel E Paul
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Dan Xie
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Luke Freyfogle
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Andrew D B Leakey
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
45
|
Wang J, Li S, Lan L, Xie M, Cheng S, Gan X, Huang G, Du G, Yu K, Ni X, Liu B, Peng G. De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance. BMC PLANT BIOLOGY 2021; 21:271. [PMID: 34118890 PMCID: PMC8196518 DOI: 10.1186/s12870-021-03003-8] [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: 11/24/2020] [Accepted: 05/04/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. RESULTS Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. CONCLUSIONS A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.
Collapse
Affiliation(s)
- Jie Wang
- Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China
| | - Shiming Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China
| | - Lei Lan
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mushan Xie
- Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shu Cheng
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaolong Gan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- Key Laboratory of Crop Molecular Breeding, Xining, 810008, Qinghai, China
| | - Gang Huang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China
| | - Guohua Du
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China
| | - Xuemei Ni
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Baolong Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.
- Key Laboratory of Crop Molecular Breeding, Xining, 810008, Qinghai, China.
| | - Guoxiong Peng
- Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| |
Collapse
|
46
|
Callegari Ferrari R, Pires Bittencourt P, Yumi Nagumo P, Silva Oliveira W, Aurineide Rodrigues M, Hartwell J, Freschi L. Developing Portulaca oleracea as a model system for functional genomics analysis of C 4/CAM photosynthesis. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:666-682. [PMID: 33256895 DOI: 10.1071/fp20202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Previously regarded as an intriguing photosynthetic curiosity, the occurrence of C4 and Crassulacean acid metabolism (CAM) photosynthesis within a single organism has recently emerged as a source of information for future biotechnological use. Among C4/CAM facultative species, Portulaca oleracea L. has been used as a model for biochemical and gene expression analysis of C4/CAM under field and laboratory conditions. In the present work, we focussed on developing molecular tools to facilitate functional genomics studies in this species, from the optimisation of RNA isolation protocols to a method for stable genetic transformation. Eleven variations of RNA extraction procedures were tested and compared for RNA quantity and quality. Also, 7 sample sets comprising total RNA from hormonal and abiotic stress treatments, distinct plant organs, leaf developmental stages, and subspecies were used to select, among 12 reference genes, the most stable reference genes for RT-qPCR analysis of each experimental condition. Furthermore, different explant sources, Agrobacterium tumefaciens strains, and regeneration and antibiotic selection media were tested in various combinations to optimise a protocol for stable genetic transformation of P. oleracea. Altogether, we provide essential tools for functional gene analysis in the context of C4/CAM photosynthesis, including an efficient RNA isolation method, preferred reference genes for RT-qPCR normalisation for a range of experimental conditions, and a protocol to produce P. oleracea stable transformants using A. tumefaciens.
Collapse
Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Priscila Pires Bittencourt
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Paula Yumi Nagumo
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Willian Silva Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Maria Aurineide Rodrigues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil; and Corresponding author.
| |
Collapse
|
47
|
Finley T, Chappell H, Veena V. Agrobacterium-Mediated Transformation of Setaria viridis, a Model System for Cereals and Bioenergy Crops. Curr Protoc 2021; 1:e127. [PMID: 33999520 DOI: 10.1002/cpz1.127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Setaria viridis is an emerging model system for the genetic and molecular characterization of cereals and bioenergy crops. Here, we describe a detailed procedure for genetic transformation of the S. viridis accession line ME034V-1. This method utilizes callus generated from mature seeds for infection with Agrobacterium tumefaciens strain AGL1 to regenerate hygromycin-resistant stable transgenic plants. It takes approximately 7 weeks to generate callus from mature seeds, 11-17 weeks from infection to the regeneration of transgenic lines, and an additional 3-4 weeks for plant growth in the greenhouse for seed collection. The protocol as presented consistently results in transformation frequency of approximately 25% for the generation of transgenic plants, with fewer escapes and higher survivability in soil for optimal seed collection. © 2021 Donald Danforth Plant Science Center. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generation of S. viridis (Accession ME034V-1) callus from mature seeds Basic Protocol 2: Agrobacterium-mediated transformation of callus to generate transgenic plants Basic Protocol 3: Plantlet transplantation in soil, plant growth in greenhouse, and seed collection Support Protocol: Preparation of Agrobacterium culture for infection.
Collapse
Affiliation(s)
- Todd Finley
- Plant Transformation Facility, Donald Danforth Plant Science Center, Saint Louis, Missouri
| | - Hal Chappell
- Plant Transformation Facility, Donald Danforth Plant Science Center, Saint Louis, Missouri
| | - Veena Veena
- Plant Transformation Facility, Donald Danforth Plant Science Center, Saint Louis, Missouri
| |
Collapse
|
48
|
Pankievicz VCS, do Amaral FP, Ané JM, Stacey G. Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:491-498. [PMID: 33543986 DOI: 10.1094/mpmi-11-20-0316-fi] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria-diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
| | - Fernanda Plucani do Amaral
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
| |
Collapse
|
49
|
da Silva VCH, Martins MCM, Calderan-Rodrigues MJ, Artins A, Monte Bello CC, Gupta S, Sobreira TJP, Riaño-Pachón DM, Mafra V, Caldana C. Shedding Light on the Dynamic Role of the "Target of Rapamycin" Kinase in the Fast-Growing C 4 Species Setaria viridis, a Suitable Model for Biomass Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:637508. [PMID: 33927734 PMCID: PMC8078139 DOI: 10.3389/fpls.2021.637508] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
The Target of Rapamycin (TOR) kinase pathway integrates energy and nutrient availability into metabolism promoting growth in eukaryotes. The overall higher efficiency on nutrient use translated into faster growth rates in C4 grass plants led to the investigation of differential transcriptional and metabolic responses to short-term chemical TOR complex (TORC) suppression in the model Setaria viridis. In addition to previously described responses to TORC inhibition (i.e., general growth arrest, translational repression, and primary metabolism reprogramming) in Arabidopsis thaliana (C3), the magnitude of changes was smaller in S. viridis, particularly regarding nutrient use efficiency and C allocation and partitioning that promote biosynthetic growth. Besides photosynthetic differences, S. viridis and A. thaliana present several specificities that classify them into distinct lineages, which also contribute to the observed alterations mediated by TOR. Indeed, cell wall metabolism seems to be distinctly regulated according to each cell wall type, as synthesis of non-pectic polysaccharides were affected in S. viridis, whilst assembly and structure in A. thaliana. Our results indicate that the metabolic network needed to achieve faster growth seems to be less stringently controlled by TORC in S. viridis.
Collapse
Affiliation(s)
| | | | | | - Anthony Artins
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Saurabh Gupta
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | | | | | - Valéria Mafra
- National Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Camila Caldana
- National Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| |
Collapse
|
50
|
Mendes Bezerra AC, da Cunha Valença D, da Gama Junqueira NE, Moll Hüther C, Borella J, Ferreira de Pinho C, Alves Ferreira M, Oliveira Medici L, Ortiz-Silva B, Reinert F. Potassium supply promotes the mitigation of NaCl-induced effects on leaf photochemistry, metabolism and morphology of Setaria viridis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:193-210. [PMID: 33513466 DOI: 10.1016/j.plaphy.2021.01.021] [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: 12/20/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Soil salinity has the potential to severely affect crop performance. To maintain cell functioning and improve salt tolerance, the maintenance of K+ homeostasis is crucial in several plant metabolism processes. Besides, potassium fertilization can efficiently alleviate the perilous effects of salinity. We characterized impacts in Setaria viridis exposed to NaCl and KCl to underlying photochemistry mechanisms, K+ and Na+ shoot contents, enzymatic activity, electrolytic leakage, and morphological responses focusing on non-stomatal limitation of photosynthesis. Plants were exposed to sodium chloride (NaCl; 0, 150 and 250 mM) and potassium chloride (KCl; 0, 5, 9 mM). The exposure to NaCl affected S. viridis leaves morphological and physiologically. Plants submitted to 150 mM showed reductions in performance indexes (PIabs and PItotal; JIP-test), and the presence of positive K- and L-bands. Plants exposed to 250 mM exhibited blockage in electron flow further than QA within 48h and permanent photoinhibition at 96 h. The presence of 9 and 5 mM of KCl counteracted the effects of NaCl on plants submitted to 150 mM, concomitant with increases in K+ accumulation and cell turgidity conservation, causing positive effects in plant growth and metabolism. Neither KCl concentrations were effective in reducing NaCl-induced effects on plants exposed to 250 mM of NaCl. Our results support the conclusion that greater availability of K+ alleviates the harmful effects of salinity in S. viridis under moderate stress and that application of KCl as means of lightning saline stress has a concentration and a salt level limit that must be experimentally determined.
Collapse
Affiliation(s)
- Ana Carolina Mendes Bezerra
- Universidade Federal Do Rio de Janeiro/IB -Dept. of Botany, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão -21941-902, Rio de Janeiro, RJ, Brazil.
| | - David da Cunha Valença
- Universidade Federal Do Rio de Janeiro/IB -Dept. of Botany, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão -21941-902, Rio de Janeiro, RJ, Brazil.
| | - Nicia Eloísa da Gama Junqueira
- Universidade Federal Do Rio de Janeiro/IB -Dept. of Botany, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão -21941-902, Rio de Janeiro, RJ, Brazil.
| | - Cristina Moll Hüther
- Universidade Federal Fluminense - Dept. of Agricultural and Environmental Engineering, R. Passo da Pátria 156, São Domingos - 24210-240 - Niterói, RJ, Brazil.
| | - Junior Borella
- Universidade Federal Do Rio Grande - Institute of Biological Sciences, Av. Itália, Km 8, Bairro Carreiros - 96203-900 - Rio Grande, RS, Brazil.
| | - Camila Ferreira de Pinho
- Universidade Federal Rural Do Rio de Janeiro - Dept. of Plant Sciences, Rod. BR 465, Km 7 - 23897-000, Seropédica, RJ, Brazil.
| | - Marcio Alves Ferreira
- Universidade Federal Do Rio de Janeiro/IB - Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão - 21941-902, Rio de Janeiro, RJ, Brazil.
| | - Leonardo Oliveira Medici
- Universidade Federal Rural Do Rio de Janeiro - Dept. of Physiological Sciences, Rod. BR 465, Km 7 - 23897-000, Seropédica, RJ, Brazil.
| | - Bianca Ortiz-Silva
- Universidade Federal Do Rio de Janeiro- NUMPEX-Bio, Estrada de Xerém, 27- Duque de Caxias - 25245-390, Rio de Janeiro, RJ, Brazil.
| | - Fernanda Reinert
- Universidade Federal Do Rio de Janeiro/IB -Dept. of Botany, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão -21941-902, Rio de Janeiro, RJ, Brazil.
| |
Collapse
|