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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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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.
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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.
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Mamidi S, Healey A, Huang P, Grimwood J, Jenkins J, Barry K, Sreedasyam A, Shu S, Lovell JT, Feldman M, Wu J, Yu Y, Chen C, Johnson J, Sakakibara H, Kiba T, Sakurai T, Tavares R, Nusinow DA, Baxter I, Schmutz J, Brutnell TP, Kellogg EA. A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nat Biotechnol 2020; 38:1203-1210. [PMID: 33020633 PMCID: PMC7536120 DOI: 10.1038/s41587-020-0681-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/24/2020] [Indexed: 11/30/2022]
Abstract
Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria viridis), a model species for studies of C4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a 'loss of shattering' trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.
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Affiliation(s)
- Sujan Mamidi
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Pu Huang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- BASF Corporation, Durham, NC, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Maximilian Feldman
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- USDA-ARS Temperate Tree Fruit and Vegetable Research Unit, Prosser, WA, USA
| | - Jinxia Wu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Cindy Chen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takatoshi Kiba
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
- Multidisciplinary Science Cluster, Kochi University, Nankoku, Kochi, Japan
| | - Rachel Tavares
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | | | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas P Brutnell
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Heslop-Harrison P. Editorial: Introducing Commentaries to Annals of Botany. ANNALS OF BOTANY 2019; 124:iv-v. [PMID: 31550046 PMCID: PMC6758579 DOI: 10.1093/aob/mcz090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Jobe TO, Zenzen I, Rahimzadeh Karvansara P, Kopriva S. Integration of sulfate assimilation with carbon and nitrogen metabolism in transition from C3 to C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4211-4221. [PMID: 31124557 PMCID: PMC6698703 DOI: 10.1093/jxb/erz250] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/21/2019] [Indexed: 05/08/2023]
Abstract
The first product of sulfate assimilation in plants, cysteine, is a proteinogenic amino acid and a source of reduced sulfur for plant metabolism. Cysteine synthesis is the convergence point of the three major pathways of primary metabolism: carbon, nitrate, and sulfate assimilation. Despite the importance of metabolic and genetic coordination of these three pathways for nutrient balance in plants, the molecular mechanisms underlying this coordination, and the sensors and signals, are far from being understood. This is even more apparent in C4 plants, where coordination of these pathways for cysteine synthesis includes the additional challenge of differential spatial localization. Here we review the coordination of sulfate, nitrate, and carbon assimilation, and show how they are altered in C4 plants. We then summarize current knowledge of the mechanisms of coordination of these pathways. Finally, we identify urgent questions to be addressed in order to understand the integration of sulfate assimilation with carbon and nitrogen metabolism particularly in C4 plants. We consider answering these questions to be a prerequisite for successful engineering of C4 photosynthesis into C3 crops to increase their efficiency.
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Affiliation(s)
- Timothy O Jobe
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Ivan Zenzen
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Parisa Rahimzadeh Karvansara
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
- Department of Biology, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Stanislav Kopriva
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
- Correspondence:
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Kumar D, Kellogg EA. Getting closer: vein density in C 4 leaves. THE NEW PHYTOLOGIST 2019; 221:1260-1267. [PMID: 30368826 DOI: 10.1111/nph.15491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/05/2018] [Indexed: 05/28/2023]
Abstract
Contents Summary 1260 I. Introduction 1260 II. Molecular and genetic mechanisms of C4 leaf venation 1262 III. Conclusions and future perspectives 1266 Acknowledgements 1266 References 1266 SUMMARY: C4 grasses are major contributors to the world's food supply. Their highly efficient method of carbon fixation is a unique adaptation that combines close vein spacing and distinct photosynthetic cell types. Despite its importance, the molecular genetic basis of C4 leaf development is still poorly understood. Here we summarize current knowledge of leaf venation and review recent progress in understanding molecular and genetic regulation of vascular patterning events in C4 plants. Evidence points to the interplay of auxin, brassinosteroids, SHORTROOT/SCARECROW and INDETERMINATE DOMAIN transcription factors. Identification and functional characterization of candidate regulators acting early in vascular development will be essential for further progress in understanding the precise regulation of these processes.
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Affiliation(s)
- Dhinesh Kumar
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
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